Ntng2 (netrin G2) - Rat Genome Database

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Gene: Ntng2 (netrin G2) Rattus norvegicus
Analyze
Symbol: Ntng2
Name: netrin G2
RGD ID: 1307089
Description: Predicted to be involved in several processes, including cell morphogenesis involved in differentiation; regulation of cell projection organization; and synapse organization. Predicted to localize to several cellular components, including Flemming body; Schaffer collateral - CA1 synapse; and anchored component of presynaptic active zone membrane. Orthologous to human NTNG2 (netrin G2); INTERACTS WITH acetamide; amphetamine; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC311836; netrin-G2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2312,492,574 - 12,551,104 (-)NCBI
Rnor_6.0 Ensembl37,742,531 - 7,796,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.037,742,511 - 7,800,834 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0313,091,083 - 13,144,474 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,171,757 - 8,225,139 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.138,172,301 - 8,230,387 (-)NCBI
Celera37,271,739 - 7,325,057 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:11804778   PMID:16980967   PMID:20382146   PMID:25411505  


Genomics

Comparative Map Data
Ntng2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2312,492,574 - 12,551,104 (-)NCBI
Rnor_6.0 Ensembl37,742,531 - 7,796,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.037,742,511 - 7,800,834 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0313,091,083 - 13,144,474 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,171,757 - 8,225,139 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.138,172,301 - 8,230,387 (-)NCBI
Celera37,271,739 - 7,325,057 (-)NCBICelera
Cytogenetic Map3p12NCBI
NTNG2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9132,161,676 - 132,244,526 (+)EnsemblGRCh38hg38GRCh38
GRCh389132,161,234 - 132,244,534 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379135,037,445 - 135,119,913 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,031,955 - 134,108,040 (+)NCBINCBI36hg18NCBI36
Build 349132,071,687 - 132,147,773NCBI
Celera9105,579,329 - 105,660,166 (+)NCBI
Cytogenetic Map9q34.13NCBI
HuRef9104,531,594 - 104,612,230 (+)NCBIHuRef
CHM1_19135,187,365 - 135,268,272 (+)NCBICHM1_1
Ntng2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39229,084,738 - 29,138,111 (-)NCBIGRCm39mm39
GRCm39 Ensembl229,084,553 - 29,143,017 (-)Ensembl
GRCm38229,194,726 - 29,248,099 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl229,194,541 - 29,253,005 (-)EnsemblGRCm38mm10GRCm38
MGSCv37229,050,341 - 29,103,560 (-)NCBIGRCm37mm9NCBIm37
MGSCv36229,016,830 - 29,070,049 (-)NCBImm8
Celera228,900,873 - 28,954,149 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map219.57NCBI
Ntng2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555131,654,398 - 1,701,062 (+)NCBIChiLan1.0ChiLan1.0
NTNG2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19131,917,736 - 131,999,801 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9131,917,760 - 131,998,107 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09103,281,915 - 103,362,786 (+)NCBIMhudiblu_PPA_v0panPan3
NTNG2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,994,593 - 52,004,620 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha951,259,084 - 51,328,052 (-)NCBI
ROS_Cfam_1.0952,887,566 - 52,956,348 (-)NCBI
UMICH_Zoey_3.1951,667,388 - 51,736,273 (-)NCBI
UNSW_CanFamBas_1.0951,992,390 - 52,061,523 (-)NCBI
UU_Cfam_GSD_1.0952,078,430 - 52,147,219 (-)NCBI
Ntng2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,010,942 - 199,069,718 (+)NCBI
SpeTri2.0NW_00493648718,779,470 - 18,838,245 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NTNG2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,011,948 - 272,077,018 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,007,513 - 272,077,105 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,097,010 - 306,136,659 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NTNG2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,897,613 - 5,978,129 (-)NCBI
ChlSab1.1 Ensembl125,899,459 - 5,972,660 (-)Ensembl
Ntng2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247604,016,441 - 4,067,325 (-)NCBI

Position Markers
RH139318  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2312,508,168 - 12,508,300 (+)MAPPER
Rnor_6.037,758,041 - 7,758,172NCBIRnor6.0
Rnor_5.0313,106,726 - 13,106,857UniSTSRnor5.0
RGSC_v3.438,187,393 - 8,187,524UniSTSRGSC3.4
Celera37,287,239 - 7,287,370UniSTS
RH 3.4 Map16192.4UniSTS
Cytogenetic Map3p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)3600086634394121Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)3565463925105730Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:57
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000045919
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.


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 2 4 11 2 56 1
Low 1 29 37 25 8 25 8 9 18 29 31 11 8
Below cutoff 14 16 16 16 6 9

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000045919   ⟹   ENSRNOP00000045926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl37,742,531 - 7,795,758 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082489   ⟹   ENSRNOP00000073450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl37,742,723 - 7,796,385 (-)Ensembl
RefSeq Acc Id: NM_001107825   ⟹   NP_001101295
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,639 - 12,545,890 (-)NCBI
Rnor_6.037,742,531 - 7,795,758 (-)NCBI
Rnor_5.0313,091,083 - 13,144,474 (-)NCBI
RGSC_v3.438,171,757 - 8,225,139 (-)RGD
Celera37,271,739 - 7,325,057 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233800   ⟹   XP_006233862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,104 (-)NCBI
Rnor_6.037,742,511 - 7,800,834 (-)NCBI
Rnor_5.0313,091,083 - 13,144,474 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591829   ⟹   XP_017447318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,104 (-)NCBI
Rnor_6.037,742,511 - 7,800,834 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591830   ⟹   XP_017447319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,549,415 (-)NCBI
Rnor_6.037,742,511 - 7,799,355 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591831   ⟹   XP_017447320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,549,853 (-)NCBI
Rnor_6.037,742,511 - 7,799,754 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591832   ⟹   XP_017447321
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,550,038 (-)NCBI
Rnor_6.037,742,511 - 7,799,954 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591833   ⟹   XP_017447322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,104 (-)NCBI
Rnor_6.037,742,511 - 7,800,834 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591834   ⟹   XP_017447323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.037,742,511 - 7,786,965 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591835   ⟹   XP_017447324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.037,742,511 - 7,795,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591836   ⟹   XP_017447325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,099 (-)NCBI
Rnor_6.037,742,511 - 7,800,832 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105225   ⟹   XP_038961153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,103 (-)NCBI
RefSeq Acc Id: XM_039105226   ⟹   XP_038961154
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,551,102 (-)NCBI
RefSeq Acc Id: XM_039105227   ⟹   XP_038961155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,545,572 (-)NCBI
RefSeq Acc Id: XM_039105228   ⟹   XP_038961156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,492,574 - 12,545,498 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101295   ⟸   NM_001107825
- Peptide Label: precursor
- UniProtKB: D4A9F4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233862   ⟸   XM_006233800
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447322   ⟸   XM_017591833
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447318   ⟸   XM_017591829
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447325   ⟸   XM_017591836
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017447321   ⟸   XM_017591832
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447320   ⟸   XM_017591831
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447319   ⟸   XM_017591830
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447324   ⟸   XM_017591835
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447323   ⟸   XM_017591834
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000045926   ⟸   ENSRNOT00000045919
RefSeq Acc Id: ENSRNOP00000073450   ⟸   ENSRNOT00000082489
RefSeq Acc Id: XP_038961153   ⟸   XM_039105225
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961154   ⟸   XM_039105226
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038961155   ⟸   XM_039105227
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038961156   ⟸   XM_039105228
- Peptide Label: isoform X4
Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
F344/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
F344/NRrrc (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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
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)
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
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
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
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/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
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 (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
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
LL/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/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
M520/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
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 (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
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)
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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
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)
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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/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
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 (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 (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
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 (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 (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/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 (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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 13093642 13093643 T C snv BUF/MNa (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307089 AgrOrtholog
Ensembl Genes ENSRNOG00000013694 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045926 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073450 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045919 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000082489 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1490 UniProtKB/TrEMBL
InterPro EGF_3 UniProtKB/TrEMBL
  EGF_laminin UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
  Laminin_N_sf UniProtKB/TrEMBL
  Sialidase_sf UniProtKB/TrEMBL
KEGG Report rno:311836 UniProtKB/TrEMBL
NCBI Gene 311836 ENTREZGENE
Pfam Laminin_EGF UniProtKB/TrEMBL
  Laminin_N UniProtKB/TrEMBL
PhenoGen Ntng2 PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_LAM_1 UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/TrEMBL
  LAMININ_NTER UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  LamNT UniProtKB/TrEMBL
Superfamily-SCOP SSF50939 UniProtKB/TrEMBL
UniProt A0A0G2K5J5_RAT UniProtKB/TrEMBL
  D4A9F4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ntng2  netrin G2   Ntng2_predicted  netrin G2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ntng2_predicted  netrin G2 (predicted)      Symbol and Name status set to approved 70820 APPROVED