Trio (trio Rho guanine nucleotide exchange factor) - Rat Genome Database

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Gene: Trio (trio Rho guanine nucleotide exchange factor) Rattus norvegicus
Analyze
Symbol: Trio
Name: trio Rho guanine nucleotide exchange factor
RGD ID: 1308360
Description: Exhibits enzyme binding activity. Predicted to be involved in negative regulation of fat cell differentiation and neuron projection morphogenesis. Predicted to localize to cell projection and cytoplasm. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability and autosomal dominant non-syndromic intellectual disability 44. Orthologous to human TRIO (trio Rho guanine nucleotide exchange factor); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC310192; triple functional domain (PTPRF interacting); triple functional domain protein
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
mRatBN7.2278,505,069 - 78,801,384 (-)NCBI
Rnor_6.0 Ensembl280,473,202 - 80,667,481 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0280,471,398 - 80,769,313 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02100,137,355 - 100,437,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4279,634,843 - 79,832,549 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1279,581,604 - 79,878,530 (-)NCBI
Celera274,141,588 - 74,436,556 (-)NCBICelera
Cytogenetic Map2q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
atropine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
casticin  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
nickel dichloride  (EXP,ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
parathion  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
tamibarotene  (ISO)
tert-butyl hydroperoxide  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
valproic acid  (EXP,ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:15669055   PMID:15715966   PMID:20519585   PMID:22666460   PMID:23230270   PMID:24859002   PMID:26323693   PMID:26721934   PMID:28928363  


Genomics

Comparative Map Data
Trio
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2278,505,069 - 78,801,384 (-)NCBI
Rnor_6.0 Ensembl280,473,202 - 80,667,481 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0280,471,398 - 80,769,313 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02100,137,355 - 100,437,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4279,634,843 - 79,832,549 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1279,581,604 - 79,878,530 (-)NCBI
Celera274,141,588 - 74,436,556 (-)NCBICelera
Cytogenetic Map2q22NCBI
TRIO
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl514,143,342 - 14,532,128 (+)EnsemblGRCh38hg38GRCh38
GRCh38514,143,342 - 14,510,204 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37514,143,451 - 14,510,313 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36514,196,829 - 14,562,458 (+)NCBINCBI36hg18NCBI36
Build 34514,196,828 - 14,562,457NCBI
Celera514,168,142 - 14,532,209 (+)NCBI
Cytogenetic Map5p15.2NCBI
HuRef514,242,473 - 14,481,695 (+)NCBIHuRef
CHM1_1514,143,936 - 14,510,180 (+)NCBICHM1_1
Trio
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391527,730,735 - 28,025,954 (-)NCBIGRCm39mm39
GRCm39 Ensembl1527,730,737 - 28,025,934 (-)Ensembl
GRCm381527,730,649 - 28,025,848 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1527,730,651 - 28,025,848 (-)EnsemblGRCm38mm10GRCm38
MGSCv371527,660,404 - 27,955,603 (-)NCBIGRCm37mm9NCBIm37
MGSCv361527,675,376 - 27,970,437 (-)NCBImm8
Celera1528,478,779 - 28,774,257 (-)NCBICelera
Cytogenetic Map15B1NCBI
Trio
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554263,646,728 - 3,846,988 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554263,647,273 - 3,846,916 (+)NCBIChiLan1.0ChiLan1.0
TRIO
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1514,417,910 - 14,655,906 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl514,423,780 - 14,654,124 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0514,448,259 - 14,814,875 (+)NCBIMhudiblu_PPA_v0panPan3
TRIO
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.134271,572 - 505,656 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl34272,290 - 505,636 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha344,764,923 - 5,120,561 (-)NCBI
ROS_Cfam_1.034182,486 - 534,192 (-)NCBI
UMICH_Zoey_3.134194,569 - 548,163 (-)NCBI
UNSW_CanFamBas_1.034194,407 - 546,539 (-)NCBI
UU_Cfam_GSD_1.034437,086 - 788,757 (-)NCBI
Trio
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213233,228,026 - 233,436,351 (-)NCBI
SpeTri2.0NW_0049366651,821,580 - 2,029,839 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRIO
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl163,563,660 - 3,921,556 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1163,690,831 - 3,921,554 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2164,216,390 - 4,261,443 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TRIO
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1413,846,753 - 14,214,647 (+)NCBI
ChlSab1.1 Ensembl413,847,936 - 14,215,164 (+)Ensembl
Trio
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475111,252,934 - 11,566,190 (+)NCBI

Position Markers
D2Rat75  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,665,616 - 78,665,758 (+)MAPPER
Rnor_6.0280,631,950 - 80,632,091NCBIRnor6.0
Rnor_5.02100,298,393 - 100,298,534UniSTSRnor5.0
RGSC_v3.4279,796,831 - 79,796,972UniSTSRGSC3.4
RGSC_v3.4279,796,790 - 79,797,113RGDRGSC3.4
RGSC_v3.1279,741,793 - 79,741,934RGD
Celera274,301,000 - 74,301,141UniSTS
RH 3.4 Map2396.9RGD
RH 3.4 Map2396.9UniSTS
RH 2.0 Map2399.9RGD
SHRSP x BN Map230.8998RGD
FHH x ACI Map236.4899RGD
Cytogenetic Map2q22UniSTS
D2Mco18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,665,619 - 78,665,763 (+)MAPPER
Rnor_6.0280,631,953 - 80,632,096NCBIRnor6.0
Rnor_5.02100,298,396 - 100,298,539UniSTSRnor5.0
RGSC_v3.4279,796,833 - 79,796,977RGDRGSC3.4
RGSC_v3.4279,796,834 - 79,796,977UniSTSRGSC3.4
RGSC_v3.1279,741,795 - 79,741,939RGD
Celera274,301,003 - 74,301,146UniSTS
Cytogenetic Map2q22UniSTS
D2Chm172  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,794,334 - 78,794,584 (+)MAPPER
Rnor_6.0280,762,019 - 80,762,268NCBIRnor6.0
Rnor_5.02100,429,269 - 100,429,518UniSTSRnor5.0
RGSC_v3.4279,927,091 - 79,927,340UniSTSRGSC3.4
Celera274,429,947 - 74,430,196UniSTS
Cytogenetic Map2q22UniSTS
D2Got381  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,580,439 - 78,580,561 (+)MAPPER
Rnor_6.0280,546,796 - 80,546,915NCBIRnor6.0
Rnor_5.02100,213,239 - 100,213,358UniSTSRnor5.0
RGSC_v3.4279,711,313 - 79,711,432UniSTSRGSC3.4
Celera274,215,838 - 74,215,957UniSTS
Cytogenetic Map2q22UniSTS
RH144049  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,532,627 - 78,532,748 (+)MAPPER
Rnor_6.0280,498,950 - 80,499,070NCBIRnor6.0
Rnor_5.02100,165,624 - 100,165,744UniSTSRnor5.0
RGSC_v3.4279,662,694 - 79,662,814UniSTSRGSC3.4
Celera274,169,077 - 74,169,197UniSTS
RH 3.4 Map2395.5UniSTS
Cytogenetic Map2q22UniSTS
RH140371  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,505,210 - 78,505,373 (+)MAPPER
Rnor_6.0280,471,540 - 80,471,702NCBIRnor6.0
Rnor_5.02100,137,497 - 100,137,659UniSTSRnor5.0
RGSC_v3.4279,634,981 - 79,635,143UniSTSRGSC3.4
Celera274,141,730 - 74,141,892UniSTS
Cytogenetic Map2q22UniSTS
RH128153  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,505,672 - 78,505,853 (+)MAPPER
Rnor_6.0280,472,002 - 80,472,182NCBIRnor6.0
Rnor_5.02100,137,959 - 100,138,139UniSTSRnor5.0
RGSC_v3.4279,635,443 - 79,635,623UniSTSRGSC3.4
Celera274,142,192 - 74,142,372UniSTS
Cytogenetic Map2q22UniSTS
RH142794  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,506,240 - 78,506,359 (+)MAPPER
Rnor_6.0280,472,570 - 80,472,688NCBIRnor6.0
Rnor_5.02100,138,527 - 100,138,645UniSTSRnor5.0
RGSC_v3.4279,636,011 - 79,636,129UniSTSRGSC3.4
Celera274,142,760 - 74,142,878UniSTS
RH 3.4 Map2394.0UniSTS
Cytogenetic Map2q22UniSTS
RH143590  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,618,167 - 78,618,294 (+)MAPPER
Rnor_6.0280,584,500 - 80,584,626NCBIRnor6.0
Rnor_5.02100,250,943 - 100,251,069UniSTSRnor5.0
RGSC_v3.4279,749,381 - 79,749,507UniSTSRGSC3.4
Celera274,253,556 - 74,253,682UniSTS
RH 3.4 Map2396.5UniSTS
Cytogenetic Map2q22UniSTS
RH143835  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,774,446 - 78,774,724 (+)MAPPER
Rnor_6.0280,742,132 - 80,742,409NCBIRnor6.0
Rnor_5.02100,409,382 - 100,409,659UniSTSRnor5.0
RGSC_v3.4279,907,204 - 79,907,481UniSTSRGSC3.4
Celera274,410,032 - 74,410,309UniSTS
RH 3.4 Map2397.8UniSTS
Cytogenetic Map2q22UniSTS
BE106322  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,698,221 - 78,698,372 (+)MAPPER
Rnor_6.0280,665,909 - 80,666,059NCBIRnor6.0
Rnor_5.02100,333,159 - 100,333,309UniSTSRnor5.0
RGSC_v3.4279,830,981 - 79,831,131UniSTSRGSC3.4
Celera274,333,391 - 74,333,541UniSTS
RH 3.4 Map2396.0UniSTS
Cytogenetic Map2q22UniSTS
BE115314  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,544,060 - 78,544,226 (+)MAPPER
Rnor_6.0280,510,380 - 80,510,545NCBIRnor6.0
Rnor_5.02100,177,054 - 100,177,219UniSTSRnor5.0
RGSC_v3.4279,674,062 - 79,674,227UniSTSRGSC3.4
Celera274,179,449 - 74,179,614UniSTS
RH 3.4 Map2397.0UniSTS
Cytogenetic Map2q22UniSTS
RH138486  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,513,320 - 78,513,484 (+)MAPPER
Rnor_6.0280,479,650 - 80,479,813NCBIRnor6.0
Rnor_5.02100,145,607 - 100,145,770UniSTSRnor5.0
RGSC_v3.4279,643,091 - 79,643,254UniSTSRGSC3.4
Celera274,149,840 - 74,150,003UniSTS
RH 3.4 Map2385.8UniSTS
Cytogenetic Map2q22UniSTS
RH139536  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,505,210 - 78,505,390 (+)MAPPER
Rnor_6.0280,471,540 - 80,471,719NCBIRnor6.0
Rnor_5.02100,137,497 - 100,137,676UniSTSRnor5.0
RGSC_v3.4279,634,981 - 79,635,160UniSTSRGSC3.4
Celera274,141,730 - 74,141,909UniSTS
RH 3.4 Map2394.1UniSTS
Cytogenetic Map2q22UniSTS
BE119929  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2278,611,740 - 78,611,910 (+)MAPPER
Rnor_6.0280,578,073 - 80,578,242NCBIRnor6.0
Rnor_5.02100,244,516 - 100,244,685UniSTSRnor5.0
RGSC_v3.4279,742,954 - 79,743,123UniSTSRGSC3.4
Celera274,247,129 - 74,247,298UniSTS
RH 3.4 Map2394.5UniSTS
Cytogenetic Map2q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)23127638105149020Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)223837491149614623Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22618609783819822Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226186097135654963Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226186097142053534Rat
12879841Cm87Cardiac mass QTL 870.026heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)227161361148295267Rat
12879842Cm88Cardiac mass QTL 880.042heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)227161361148295267Rat
12879843Am3Aortic mass QTL 30.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)227161361148295267Rat
12879844Kidm62Kidney mass QTL 620.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227161361148295267Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23408817591101903Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)236245223112175725Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240171834105089682Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916169852800Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243141290114164944Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243141290114164944Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243141290154583160Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)24314978885642672Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)260131410135646395Rat
5684990Bmd82Bone mineral density QTL 822.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)260325352106432915Rat
5684996Bmd85Bone mineral density QTL 854.70.024tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)260325352106432915Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)260325352147522851Rat
631500Bp99Blood pressure QTL 992.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)260325686105059293Rat
1578777Stresp15Stress response QTL 1520.05blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)261924251106924251Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)26886541480632096Rat
1581576Pur7Proteinuria QTL 70.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)26886541480632096Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)268865414169852800Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)26886645480631953Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)268866454149614466Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)270132175115132175Rat
2317041Aia14Adjuvant induced arthritis QTL 143.29joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)271495404116495404Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)27568749596556760Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)27568749596556760Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)278321410105089682Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)278321410105089682Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278321410158159410Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)280631950149614623Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:37
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000016784, ENSRNOT00000049793
Prediction methods: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.


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 34 24 12 12 12 8 8 74 29 34 11 8
Low 3 9 33 29 7 29 3 6 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003749226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003753540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BF522721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ211464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB546429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016784   ⟹   ENSRNOP00000016784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl280,473,202 - 80,667,481 (-)Ensembl
RefSeq Acc Id: NM_001107658   ⟹   NP_001101128
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2278,505,069 - 78,801,207 (-)NCBI
RefSeq Acc Id: XM_003749226   ⟹   XP_003749274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0280,471,398 - 80,769,313 (-)NCBI
Rnor_5.02100,137,355 - 100,437,964 (-)NCBI
Sequence:
RefSeq Acc Id: XM_003753540   ⟹   XP_003753588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera274,141,588 - 74,436,511 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006224052   ⟹   XP_006224114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera274,141,588 - 74,436,556 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006224053   ⟹   XP_006224115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera274,143,392 - 74,436,445 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232090   ⟹   XP_006232152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2278,505,069 - 78,801,384 (-)NCBI
Rnor_6.0280,471,398 - 80,769,313 (-)NCBI
Rnor_5.02100,137,355 - 100,437,964 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232091   ⟹   XP_006232153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2278,505,069 - 78,800,738 (-)NCBI
Rnor_6.0280,473,202 - 80,767,997 (-)NCBI
Rnor_5.02100,137,355 - 100,437,964 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591212   ⟹   XP_017446701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2278,517,118 - 78,801,384 (-)NCBI
Rnor_6.0280,483,497 - 80,769,312 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591213   ⟹   XP_017446702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0280,510,474 - 80,769,311 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595073   ⟹   XP_017450562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera274,153,687 - 74,436,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595074   ⟹   XP_017450563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera274,179,543 - 74,436,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102226   ⟹   XP_038958154
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2278,505,069 - 78,649,651 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_003749274   ⟸   XM_003749226
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_003753588   ⟸   XM_003753540
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006224114   ⟸   XM_006224052
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006224115   ⟸   XM_006224053
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006232152   ⟸   XM_006232090
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006232153   ⟸   XM_006232091
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450562   ⟸   XM_017595073
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017450563   ⟸   XM_017595074
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017446701   ⟸   XM_017591212
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017446702   ⟸   XM_017591213
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000016784   ⟸   ENSRNOT00000016784
RefSeq Acc Id: NP_001101128   ⟸   NM_001107658
RefSeq Acc Id: XP_038958154   ⟸   XM_039102226
- Peptide Label: isoform X3
Protein Domains
CRAL-TRIO   DH   Ig-like   Ig-like C2-type   PH   Protein kinase   SH3

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)
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
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)
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
LE/Stm (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
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)
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
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)
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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)
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
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
2 100153706 100153707 G A snv BUF/N (KNAW)
2 100310535 100310536 C T snv DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 80487528 80487529 C A snv LE/Stm (RGD)
2 80487749 80487750 G A snv Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308360 AgrOrtholog
Ensembl Genes ENSRNOG00000012148 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016784 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016784 UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.525.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CRAL-TRIO_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL-TRIO_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DBL_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DH-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 310192 ENTREZGENE
PANTHER PTHR22826:SF104 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Trio PhenoGen
PROSITE CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DH_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEC14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPEC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48065 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1P0PBZ6_RAT UniProtKB/TrEMBL
  F1M0Z1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-02 Trio  trio Rho guanine nucleotide exchange factor  Trio  triple functional domain (PTPRF interacting)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Trio  triple functional domain (PTPRF interacting)  Trio_predicted  triple functional domain (PTPRF interacting) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Trio_predicted  triple functional domain (PTPRF interacting) (predicted)      Symbol and Name status set to approved 70820 APPROVED