Ntn3 (netrin 3) - Rat Genome Database

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Gene: Ntn3 (netrin 3) Rattus norvegicus
Analyze
Symbol: Ntn3
Name: netrin 3
RGD ID: 619811
Description: Predicted to enable signaling receptor binding activity. Predicted to be involved in animal organ morphogenesis; neuron projection development; and tissue development. Predicted to be located in Golgi apparatus and extracellular region. Predicted to be active in basement membrane. Orthologous to human NTN3 (netrin 3); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: netrin 2-like; netrin 2-like (chicken); netrin-3; Ntn2l
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81013,741,459 - 13,744,555 (-)NCBIGRCr8
mRatBN7.21013,236,905 - 13,240,001 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,236,905 - 13,240,001 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1017,981,701 - 17,984,797 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,470,540 - 17,473,636 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01012,969,384 - 12,972,480 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01013,577,725 - 13,580,821 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,577,725 - 13,580,821 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01013,393,760 - 13,396,856 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41013,457,653 - 13,460,749 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11013,459,137 - 13,460,207 (-)NCBI
Celera1012,922,863 - 12,925,959 (-)NCBICelera
Cytogenetic Map10q12NCBI
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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Widespread expression of netrin-1 by neurons and oligodendrocytes in the adult mammalian spinal cord. Manitt C, etal., J Neurosci 2001 Jun 1;21(11):3911-22.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10366627   PMID:10381568   PMID:15520228  


Genomics

Comparative Map Data
Ntn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81013,741,459 - 13,744,555 (-)NCBIGRCr8
mRatBN7.21013,236,905 - 13,240,001 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1013,236,905 - 13,240,001 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1017,981,701 - 17,984,797 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01017,470,540 - 17,473,636 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01012,969,384 - 12,972,480 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01013,577,725 - 13,580,821 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,577,725 - 13,580,821 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01013,393,760 - 13,396,856 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41013,457,653 - 13,460,749 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11013,459,137 - 13,460,207 (-)NCBI
Celera1012,922,863 - 12,925,959 (-)NCBICelera
Cytogenetic Map10q12NCBI
NTN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38162,471,297 - 2,474,145 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl162,471,297 - 2,474,145 (+)EnsemblGRCh38hg38GRCh38
GRCh37162,521,298 - 2,524,146 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36162,461,501 - 2,464,147 (+)NCBINCBI36Build 36hg18NCBI36
Build 34162,461,500 - 2,464,147NCBI
Celera162,735,875 - 2,738,521 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef162,446,819 - 2,449,530 (+)NCBIHuRef
CHM1_1162,521,394 - 2,524,040 (+)NCBICHM1_1
T2T-CHM13v2.0162,493,427 - 2,496,275 (+)NCBIT2T-CHM13v2.0
Ntn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391724,422,805 - 24,428,361 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1724,422,822 - 24,428,505 (-)EnsemblGRCm39 Ensembl
GRCm381724,203,831 - 24,209,387 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1724,203,848 - 24,209,531 (-)EnsemblGRCm38mm10GRCm38
MGSCv371724,340,776 - 24,346,332 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361723,931,431 - 23,936,987 (-)NCBIMGSCv36mm8
Celera1724,709,264 - 24,714,824 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.31NCBI
Ntn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544214,838,076 - 14,840,857 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544214,838,076 - 14,840,857 (-)NCBIChiLan1.0ChiLan1.0
NTN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2182,966,446 - 2,976,169 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1166,747,344 - 6,756,826 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0161,323,148 - 1,330,713 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1162,570,954 - 2,574,943 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl162,571,072 - 2,573,173 (+)Ensemblpanpan1.1panPan2
NTN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,558,942 - 38,561,437 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl638,558,150 - 38,561,323 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha639,797,130 - 39,799,511 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0638,868,001 - 38,870,384 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl638,868,001 - 38,870,384 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1638,553,133 - 38,555,514 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0638,525,757 - 38,528,138 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,001,909 - 39,004,291 (-)NCBIUU_Cfam_GSD_1.0
Ntn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,123,480 - 105,145,788 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366941,582,643 - 1,585,455 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366941,581,322 - 1,585,893 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NTN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl339,572,531 - 39,575,170 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1339,572,430 - 39,575,717 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2342,610,519 - 42,629,599 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NTN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.152,349,614 - 2,353,197 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl52,350,797 - 2,353,184 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606828,684,323 - 28,687,245 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ntn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624824221,724 - 225,260 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624824221,296 - 244,014 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ntn3
5 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:37
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000009735
Prediction methods:Microtar, Miranda, Rnahybrid
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat


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 6 18
Low 24 17 11 2 11 1 1 74 16 15 4 1
Below cutoff 3 16 35 30 10 30 5 8 10 7 7 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009735   ⟹   ENSRNOP00000009735
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1013,236,905 - 13,240,001 (-)Ensembl
Rnor_6.0 Ensembl1013,577,725 - 13,580,821 (-)Ensembl
RefSeq Acc Id: NM_053732   ⟹   NP_446184
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81013,741,459 - 13,744,555 (-)NCBI
mRatBN7.21013,236,905 - 13,240,001 (-)NCBI
Rnor_6.01013,577,725 - 13,580,821 (-)NCBI
Rnor_5.01013,393,760 - 13,396,856 (-)NCBI
RGSC_v3.41013,457,653 - 13,460,749 (-)RGD
Celera1012,922,863 - 12,925,959 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446184 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK17015 (Get FASTA)   NCBI Sequence Viewer  
  EDM03814 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009735
  ENSRNOP00000009735.1
Reference Protein Sequences
RefSeq Acc Id: NP_446184   ⟸   NM_053732
- Peptide Label: precursor
- UniProtKB: G3V6X3 (UniProtKB/TrEMBL),   A6HCQ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009735   ⟸   ENSRNOT00000009735
Protein Domains
Laminin EGF-like   Laminin N-terminal   NTR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6X3-F1-model_v2 AlphaFold G3V6X3 1-580 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:619811 AgrOrtholog
BioCyc Gene G2FUF-25871 BioCyc
Ensembl Genes ENSRNOG00000006970 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009735 ENTREZGENE
  ENSRNOT00000009735.4 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.120 UniProtKB/TrEMBL
  Galactose-binding domain-like UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro EGF_laminin UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  Netrin_domain UniProtKB/TrEMBL
  Netrin_module_non-TIMP UniProtKB/TrEMBL
  TIMP-like_OB-fold UniProtKB/TrEMBL
KEGG Report rno:114524 UniProtKB/TrEMBL
NCBI Gene 114524 ENTREZGENE
PANTHER NETRIN/LAMININ-RELATED UniProtKB/TrEMBL
  PTHR10574:SF443 UniProtKB/TrEMBL
Pfam Laminin_EGF UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  NTR UniProtKB/TrEMBL
PhenoGen Ntn3 PhenoGen
PROSITE EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  LAMININ_NTER UniProtKB/TrEMBL
  NTR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006970 RatGTEx
SMART C345C UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  LamNT UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  TIMP_like UniProtKB/TrEMBL
UniProt A6HCQ9 ENTREZGENE, UniProtKB/TrEMBL
  G3V6X3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Ntn3  netrin 3  Ntn2l  netrin 2-like (chicken)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ntn2l  netrin 2-like (chicken)  Ntn3  Netrin 3  Symbol and Name updated 1299863 APPROVED
2005-01-20 Ntn3  Netrin 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Ntn3  Netrin 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the embryonic spinal cord 633501
gene_product member of the netrin family of secreted proteins 633501