Nav2 (neuron navigator 2) - Rat Genome Database

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Gene: Nav2 (neuron navigator 2) Rattus norvegicus
Analyze
Symbol: Nav2
Name: neuron navigator 2
RGD ID: 619778
Description: Predicted to have 3'-5' DNA helicase activity and heparin binding activity. Involved in nervous system development. Predicted to localize to interstitial matrix and nucleoplasm. Orthologous to human NAV2 (neuron navigator 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC361581; Rainb1; retinoic acid inducible in neuroblastoma cells 1
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
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
Rnor_6.0 Ensembl1104,576,589 - 104,941,552 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01104,575,765 - 104,941,554 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01105,340,947 - 105,994,390 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4199,041,044 - 99,410,077 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1199,329,852 - 99,330,326 (+)NCBI
Celera193,160,898 - 93,522,785 (+)NCBICelera
Cytogenetic Map1q22NCBI
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-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
isobutanol  (ISO)
leflunomide  (ISO)
manganese(II) chloride  (EXP)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (ISO)
potassium dichromate  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
Soman  (EXP)
succimer  (ISO)
tamoxifen  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:15158073   PMID:18757743   PMID:20184720   PMID:21419114  


Genomics

Comparative Map Data
Nav2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
Rnor_6.0 Ensembl1104,576,589 - 104,941,552 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01104,575,765 - 104,941,554 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01105,340,947 - 105,994,390 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4199,041,044 - 99,410,077 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1199,329,852 - 99,330,326 (+)NCBI
Celera193,160,898 - 93,522,785 (+)NCBICelera
Cytogenetic Map1q22NCBI
NAV2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1119,350,724 - 20,121,601 (+)EnsemblGRCh38hg38GRCh38
GRCh381119,345,200 - 20,121,601 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371119,366,783 - 20,143,147 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361119,691,488 - 20,099,723 (+)NCBINCBI36hg18NCBI36
Build 341119,691,487 - 20,099,722NCBI
Celera1119,505,019 - 20,275,779 (+)NCBI
Cytogenetic Map11p15.1NCBI
HuRef1119,056,089 - 19,826,507 (+)NCBIHuRef
CHM1_11119,371,529 - 20,143,061 (+)NCBICHM1_1
Nav2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39748,608,796 - 49,259,838 (+)NCBIGRCm39mm39
GRCm39 Ensembl748,558,464 - 49,259,838 (+)Ensembl
GRCm38748,959,063 - 49,610,090 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl748,908,716 - 49,610,090 (+)EnsemblGRCm38mm10GRCm38
MGSCv37756,214,443 - 56,865,458 (+)NCBIGRCm37mm9NCBIm37
MGSCv36749,232,742 - 49,322,663 (+)NCBImm8
Celera744,402,885 - 45,057,893 (+)NCBICelera
Cytogenetic Map7B4NCBI
Nav2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955476613,512 - 996,535 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955476614,215 - 996,450 (+)NCBIChiLan1.0ChiLan1.0
NAV2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11119,288,369 - 20,055,758 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1119,288,598 - 20,055,758 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01119,370,095 - 20,143,255 (+)NCBIMhudiblu_PPA_v0panPan3
NAV2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12141,458,280 - 42,181,227 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2141,458,984 - 42,177,813 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2140,930,438 - 41,658,542 (+)NCBI
ROS_Cfam_1.02142,575,579 - 43,302,697 (+)NCBI
UMICH_Zoey_3.12141,906,748 - 42,305,151 (+)NCBI
UNSW_CanFamBas_1.02141,760,150 - 42,480,872 (+)NCBI
UU_Cfam_GSD_1.02142,137,560 - 42,861,640 (+)NCBI
Nav2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494742,807,521 - 43,503,750 (-)NCBI
SpeTri2.0NW_004936654740,270 - 1,119,065 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NAV2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl239,266,913 - 40,077,925 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1239,263,939 - 40,083,539 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2242,202,180 - 42,246,214 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NAV2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1144,887,172 - 45,648,260 (-)NCBI
ChlSab1.1 Ensembl144,887,169 - 45,214,703 (-)Ensembl
Nav2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476611,056,877 - 11,417,291 (+)NCBI

Position Markers
D1Rat102  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,141,112 - 99,141,287 (+)MAPPER
Rnor_6.01104,759,738 - 104,759,912NCBIRnor6.0
Rnor_5.01105,814,136 - 105,814,310UniSTSRnor5.0
RGSC_v3.4199,224,208 - 99,224,690RGDRGSC3.4
RGSC_v3.4199,224,444 - 99,224,618UniSTSRGSC3.4
RGSC_v3.1199,302,555 - 99,302,729RGD
Celera193,343,398 - 93,343,572UniSTS
RH 3.4 Map1922.4UniSTS
RH 3.4 Map1922.4RGD
RH 2.0 Map1601.7RGD
FHH x ACI Map150.0RGD
Cytogenetic Map1q22UniSTS
D1Rat465  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,107,258 - 99,107,381 (+)MAPPER
Rnor_6.01104,725,891 - 104,726,013NCBIRnor6.0
Rnor_5.01105,780,289 - 105,780,411UniSTSRnor5.0
RGSC_v3.4199,190,249 - 99,190,372RGDRGSC3.4
RGSC_v3.4199,190,250 - 99,190,372UniSTSRGSC3.4
RGSC_v3.1199,268,360 - 99,268,483RGD
Celera193,309,562 - 93,309,684UniSTS
FHH x ACI Map149.52RGD
FHH x ACI Map149.52UniSTS
Cytogenetic Map1q22UniSTS
D1Got99  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,063,515 - 99,063,672 (+)MAPPER
Rnor_6.01104,681,748 - 104,681,904NCBIRnor6.0
Rnor_5.01105,736,323 - 105,736,479UniSTSRnor5.0
RGSC_v3.4199,146,344 - 99,146,501RGDRGSC3.4
RGSC_v3.4199,146,345 - 99,146,501UniSTSRGSC3.4
RGSC_v3.1199,224,455 - 99,224,612RGD
Celera193,266,014 - 93,266,170UniSTS
RH 3.4 Map1917.3UniSTS
RH 3.4 Map1917.3RGD
RH 2.0 Map1603.7RGD
Cytogenetic Map1q22UniSTS
36.MMHAP29FRD12.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2198,958,493 - 98,958,575 (+)MAPPER
Rnor_6.01104,576,685 - 104,576,766NCBIRnor6.0
Rnor_5.01105,631,418 - 105,631,499UniSTSRnor5.0
RGSC_v3.4199,041,140 - 99,041,221UniSTSRGSC3.4
Celera193,160,994 - 93,161,075UniSTS
Cytogenetic Map1q22UniSTS
RH141496  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,319,134 - 99,319,329 (+)MAPPER
Rnor_6.01104,938,350 - 104,938,544NCBIRnor6.0
Rnor_5.01105,991,186 - 105,991,380UniSTSRnor5.0
RGSC_v3.4199,406,875 - 99,407,069UniSTSRGSC3.4
Celera193,519,582 - 93,519,776UniSTS
RH 3.4 Map1921.0UniSTS
Cytogenetic Map1q22UniSTS
BI288607  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,299,259 - 99,299,457 (+)MAPPER
Rnor_6.01104,918,332 - 104,918,529NCBIRnor6.0
Rnor_5.01105,971,168 - 105,971,365UniSTSRnor5.0
RGSC_v3.4199,387,018 - 99,387,215UniSTSRGSC3.4
Celera193,499,704 - 93,499,901UniSTS
RH 3.4 Map1922.4UniSTS
Cytogenetic Map1q22UniSTS
RH135248  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,040,653 - 99,040,855 (+)MAPPER
Rnor_6.01104,658,902 - 104,659,103NCBIRnor6.0
Rnor_5.01105,713,635 - 105,713,836UniSTSRnor5.0
RGSC_v3.4199,123,507 - 99,123,708UniSTSRGSC3.4
Celera193,243,159 - 93,243,360UniSTS
RH 3.4 Map1918.8UniSTS
Cytogenetic Map1q22UniSTS
RH138789  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,208,188 - 99,208,338 (+)MAPPER
Rnor_6.01104,827,341 - 104,827,490NCBIRnor6.0
Rnor_5.01105,880,529 - 105,880,678UniSTSRnor5.0
RGSC_v3.4199,293,626 - 99,293,775UniSTSRGSC3.4
Celera193,409,027 - 93,409,176UniSTS
RH 3.4 Map1920.7UniSTS
Cytogenetic Map1q22UniSTS
BQ195500  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2198,976,840 - 98,976,995 (+)MAPPER
Rnor_6.01104,595,024 - 104,595,178NCBIRnor6.0
Rnor_5.01105,649,757 - 105,649,911UniSTSRnor5.0
RGSC_v3.4199,059,756 - 99,059,910UniSTSRGSC3.4
Celera193,179,350 - 93,179,504UniSTS
RH 3.4 Map1912.29UniSTS
Cytogenetic Map1q22UniSTS
UniSTS:498520  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,309,776 - 99,310,542 (+)MAPPER
Rnor_6.01104,928,854 - 104,929,619NCBIRnor6.0
Rnor_5.01105,981,690 - 105,982,455UniSTSRnor5.0
RGSC_v3.4199,397,532 - 99,398,297UniSTSRGSC3.4
Celera193,510,222 - 93,510,987UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:818
Count of miRNA genes:289
Interacting mature miRNAs:362
Transcripts:ENSRNOT00000046529
Prediction methods:Microtar, Miranda, 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 30 16 14 14 62 35 27 11
Low 3 13 41 27 19 27 8 11 12 14 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588747 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588748 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF466145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000046529   ⟹   ENSRNOP00000051474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1104,576,589 - 104,941,552 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078477   ⟹   ENSRNOP00000074453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1104,635,989 - 104,940,171 (+)Ensembl
RefSeq Acc Id: NM_138529   ⟹   NP_612538
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,958,398 - 99,322,337 (+)NCBI
Rnor_6.01104,576,589 - 104,941,552 (+)NCBI
Rnor_5.01105,340,947 - 105,994,390 (+)NCBI
RGSC_v3.4199,041,044 - 99,410,077 (+)RGD
Celera193,160,898 - 93,522,785 (+)RGD
Sequence:
RefSeq Acc Id: XM_006229244   ⟹   XP_006229306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,635,622 - 104,941,554 (+)NCBI
Rnor_5.01105,340,947 - 105,994,390 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008759315   ⟹   XP_008757537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,783,207 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588740   ⟹   XP_017444229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
Rnor_6.01104,575,766 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588741   ⟹   XP_017444230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
Rnor_6.01104,575,766 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588742   ⟹   XP_017444231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,575,766 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588743   ⟹   XP_017444232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,958,398 - 99,322,339 (+)NCBI
Rnor_6.01104,575,766 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588744   ⟹   XP_017444233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,575,767 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588745   ⟹   XP_017444234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,575,767 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588746   ⟹   XP_017444235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,730,440 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588747   ⟹   XP_017444236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,730,429 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588748   ⟹   XP_017444237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,744,386 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588749   ⟹   XP_017444238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01104,575,765 - 104,941,554 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091525   ⟹   XP_038947453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
RefSeq Acc Id: XM_039091528   ⟹   XP_038947456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
RefSeq Acc Id: XM_039091615   ⟹   XP_038947543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,322,339 (+)NCBI
RefSeq Acc Id: XR_005492904
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2198,957,629 - 99,303,233 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_612538   ⟸   NM_138529
- UniProtKB: F1LR12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229306   ⟸   XM_006229244
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008757537   ⟸   XM_008759315
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017444238   ⟸   XM_017588749
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017444229   ⟸   XM_017588740
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444230   ⟸   XM_017588741
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017444231   ⟸   XM_017588742
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017444232   ⟸   XM_017588743
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017444233   ⟸   XM_017588744
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017444234   ⟸   XM_017588745
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017444236   ⟸   XM_017588747
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017444235   ⟸   XM_017588746
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017444237   ⟸   XM_017588748
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000074453   ⟸   ENSRNOT00000078477
RefSeq Acc Id: ENSRNOP00000051474   ⟸   ENSRNOT00000046529
RefSeq Acc Id: XP_038947453   ⟸   XM_039091525
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947456   ⟸   XM_039091528
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947543   ⟸   XM_039091615
- Peptide Label: isoform X5
Protein Domains
Calponin-homology (CH)

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)
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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 (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/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 (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)
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
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
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)
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
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)
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
SS/Jr (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
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)
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
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)
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
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)
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
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
1 105935210 105935211 C T snv SR/JrHsd (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW)
1 105988432 105988433 C A snv GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
1 105988535 105988536 A C snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 104935596 104935597 C A snv GH/OmrMcwi (MCW), F344/NCrl (RGD), SS/Jr (RGD), SR/JrHsd (RGD), LL/MavRrrc (RGD), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), MR/N (MCW), WN/N (MCW), SS/JrHsdMcwi (RGD), LE/Stm (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD)
1 104935699 104935700 A C snv FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 99350622 99350623 C T snv FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SR/JrHsd (MCW)
1 99404121 99404122 C A snv WN/N (KNAW), MR/N (KNAW), F344/NHsd (ICAHN), SS/JrHsdMcwi (MDC), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), F344/NCrl (ICL), LE/Stm (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL)
1 99404224 99404225 A C snv FHH/EurMcwi (ICL), FHH/EurMcwi (MDC), FHL/EurMcwi (ICL), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619778 AgrOrtholog
Ensembl Genes ENSRNOG00000014530 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051474 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074453 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046529 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078477 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/TrEMBL
  Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  Nav/unc-53 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:171563 UniProtKB/TrEMBL
NCBI Gene 171563 ENTREZGENE
PANTHER PTHR12784 UniProtKB/TrEMBL
Pfam PF00307 UniProtKB/TrEMBL
PhenoGen Nav2 PhenoGen
PROSITE PS50021 UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
  SM00033 UniProtKB/TrEMBL
Superfamily-SCOP Calponin-homology UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2K833_RAT UniProtKB/TrEMBL
  F1LR12 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-28 Nav2  neuron navigator 2  Rainb1  retinoic acid inducible in neuroblastoma cells 1  Symbol and Name updated 1299863 APPROVED
2006-04-28 Rainb1  retinoic acid inducible in neuroblastoma cells 1  Nav2_predicted  neuron navigator 2 (predicted)  Data Merged 737654 APPROVED
2005-01-20 Rainb1  retinoic acid inducible in neuroblastoma cells 1      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Nav2_predicted  neuron navigator 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Rainb1  retinoic acid inducible in neuroblastoma cells 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology has high similarity to C. elegans unc-53, which is required for axon elongation of mechanosensory neurons 633822