Inpp4b (inositol polyphosphate-4-phosphatase type II B) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Inpp4b (inositol polyphosphate-4-phosphatase type II B) Rattus norvegicus
Analyze
Symbol: Inpp4b
Name: inositol polyphosphate-4-phosphatase type II B
RGD ID: 620470
Description: Enables phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity. Acts upstream of or within inositol phosphate dephosphorylation and phosphatidylinositol dephosphorylation. Predicted to be located in Golgi apparatus. Predicted to be active in cytoplasm. Orthologous to human INPP4B (inositol polyphosphate-4-phosphatase type II B); PARTICIPATES IN inositol phosphate metabolic pathway; phosphoinositide metabolic pathway; phosphatidylinositol 3-kinase signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: inositol polyphosphate 4-phosphatase type II; inositol polyphosphate-4-phosphatase type II 105kD; inositol polyphosphate-4-phosphatase, type II; inositol polyphosphate-4-phosphatase, type II, 105kD; type II inositol 3,4-bisphosphate 4-phosphatase; type II inositol-3,4-bisphosphate 4-phosphatase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Inpp4bTn(sb-T2/Bart3)2.143Mcwi   Inpp4bTn(sb-T2/Bart3)2.232Mcwi  
Genetic Models: F344-Inpp4bTn(sb-T2/Bart3)2.232Mcwi F344-Inpp4bTn(sb-T2/Bart3)2.143Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21925,920,189 - 26,670,085 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1925,925,358 - 26,280,634 (-)Ensembl
Rnor_6.01929,592,889 - 30,341,528 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1929,597,905 - 29,968,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01940,508,684 - 41,132,035 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41927,722,430 - 28,363,639 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11927,727,256 - 28,484,803 (-)NCBI
Celera1925,451,220 - 26,189,580 (-)NCBICelera
Cytogenetic Map19q11NCBI
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
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
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-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP,ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
daunorubicin  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
folpet  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
hydroquinone  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
isotretinoin  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
O-methyleugenol  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tetrachloromethane  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:16631325   PMID:21982707   PMID:23078915  


Genomics

Comparative Map Data
Inpp4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21925,920,189 - 26,670,085 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1925,925,358 - 26,280,634 (-)Ensembl
Rnor_6.01929,592,889 - 30,341,528 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1929,597,905 - 29,968,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01940,508,684 - 41,132,035 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41927,722,430 - 28,363,639 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11927,727,256 - 28,484,803 (-)NCBI
Celera1925,451,220 - 26,189,580 (-)NCBICelera
Cytogenetic Map19q11NCBI
INPP4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4142,023,160 - 142,847,432 (-)EnsemblGRCh38hg38GRCh38
GRCh384142,023,160 - 142,846,535 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374142,944,313 - 143,767,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364143,168,631 - 143,987,054 (-)NCBINCBI36hg18NCBI36
Build 344143,307,498 - 143,710,137NCBI
Celera4140,279,978 - 141,098,274 (-)NCBI
Cytogenetic Map4q31.21NCBI
HuRef4138,678,404 - 139,496,966 (-)NCBIHuRef
CHM1_14142,926,560 - 143,744,866 (-)NCBICHM1_1
Inpp4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39882,068,895 - 82,865,553 (+)NCBIGRCm39mm39
GRCm39 Ensembl882,069,185 - 82,854,543 (+)Ensembl
GRCm38881,342,266 - 82,134,312 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl881,342,556 - 82,127,914 (+)EnsemblGRCm38mm10GRCm38
MGSCv37884,239,099 - 84,646,460 (+)NCBIGRCm37mm9NCBIm37
MGSCv36884,610,947 - 85,018,308 (+)NCBImm8
Celera886,003,317 - 86,422,617 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map839.02NCBI
Inpp4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955471938,005 - 1,291,695 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955471938,005 - 1,291,695 (+)NCBIChiLan1.0ChiLan1.0
INPP4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14145,707,005 - 146,513,611 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4145,706,307 - 146,141,029 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04134,405,934 - 135,213,851 (-)NCBIMhudiblu_PPA_v0panPan3
INPP4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.119826,711 - 1,192,340 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl19850,784 - 1,186,498 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha191,074,484 - 1,439,447 (+)NCBI
ROS_Cfam_1.019847,593 - 1,213,382 (+)NCBI
UMICH_Zoey_3.119829,445 - 1,194,997 (+)NCBI
UNSW_CanFamBas_1.0191,190,522 - 1,556,374 (+)NCBI
UU_Cfam_GSD_1.0191,544,331 - 1,910,402 (+)NCBI
Inpp4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530147,989,723 - 48,731,310 (+)NCBI
SpeTri2.0NW_0049365355,427,131 - 6,168,622 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
INPP4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl884,811,772 - 85,514,518 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1884,812,041 - 85,555,200 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2890,440,950 - 90,810,384 (+)NCBISscrofa10.2Sscrofa10.2susScr3
INPP4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1788,929,249 - 89,732,375 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl788,979,493 - 89,461,475 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603768,478,295 - 69,289,053 (-)NCBIVero_WHO_p1.0
Inpp4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248531,350,577 - 2,147,616 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D15Mit4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25138,497,366 - 138,497,449 (+)MAPPERmRatBN7.2
mRatBN7.25138,493,166 - 138,493,249 (+)MAPPERmRatBN7.2
mRatBN7.21926,052,677 - 26,052,794 (+)MAPPERmRatBN7.2
mRatBN7.25138,501,566 - 138,501,649 (+)MAPPERmRatBN7.2
mRatBN7.25138,505,766 - 138,505,849 (+)MAPPERmRatBN7.2
Rnor_6.01929,725,257 - 29,725,373NCBIRnor6.0
Rnor_6.05144,227,288 - 144,227,370NCBIRnor6.0
Rnor_5.01940,635,255 - 40,635,371UniSTSRnor5.0
Rnor_5.05147,995,326 - 147,995,408UniSTSRnor5.0
RGSC_v3.45145,575,830 - 145,575,912UniSTSRGSC3.4
RGSC_v3.41927,849,593 - 27,849,709UniSTSRGSC3.4
RGSC_v3.11927,854,418 - 27,854,535RGD
Celera1925,576,861 - 25,576,977UniSTS
Celera5137,003,287 - 137,003,369UniSTS
Cytogenetic Map19q11UniSTS
D19Rat41  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,296,511 - 26,296,662 (+)MAPPERmRatBN7.2
Rnor_6.01929,966,560 - 29,966,710NCBIRnor6.0
Rnor_5.01940,875,102 - 40,875,252UniSTSRnor5.0
RGSC_v3.41928,102,830 - 28,102,981RGDRGSC3.4
RGSC_v3.41928,102,831 - 28,102,981UniSTSRGSC3.4
RGSC_v3.11928,107,656 - 28,107,807RGD
Celera1925,818,951 - 25,819,101UniSTS
SHRSP x BN Map1920.2599RGD
SHRSP x BN Map1920.2599UniSTS
Cytogenetic Map19q11UniSTS
D19Rat120  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,182,615 - 26,182,815 (+)MAPPERmRatBN7.2
Rnor_6.01929,855,156 - 29,855,355NCBIRnor6.0
Rnor_5.01940,765,631 - 40,765,830UniSTSRnor5.0
RGSC_v3.41927,980,182 - 27,980,382RGDRGSC3.4
RGSC_v3.41927,980,183 - 27,980,382UniSTSRGSC3.4
RGSC_v3.11927,985,008 - 27,985,208RGD
Celera1925,706,606 - 25,706,805UniSTS
SHRSP x BN Map1920.2599RGD
SHRSP x BN Map1920.2599UniSTS
Cytogenetic Map19q11UniSTS
D19Got19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,283,898 - 26,284,096 (+)MAPPERmRatBN7.2
Rnor_6.01929,954,758 - 29,954,955NCBIRnor6.0
Rnor_5.01940,863,300 - 40,863,497UniSTSRnor5.0
RGSC_v3.41928,089,765 - 28,089,963RGDRGSC3.4
RGSC_v3.41928,089,766 - 28,089,963UniSTSRGSC3.4
RGSC_v3.11928,094,591 - 28,094,789RGD
Celera1925,806,321 - 25,806,518UniSTS
Cytogenetic Map19q11UniSTS
AU047006  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,551,265 - 26,551,402 (+)MAPPERmRatBN7.2
Rnor_6.01930,221,722 - 30,221,858NCBIRnor6.0
Rnor_5.01941,130,850 - 41,130,986UniSTSRnor5.0
RGSC_v3.41928,362,454 - 28,362,590UniSTSRGSC3.4
Celera1926,073,432 - 26,073,568UniSTS
Cytogenetic Map19q11UniSTS
RH138607  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,236,741 - 26,236,960 (+)MAPPERmRatBN7.2
Rnor_6.01929,908,062 - 29,908,280NCBIRnor6.0
Rnor_5.01940,816,604 - 40,816,822UniSTSRnor5.0
RGSC_v3.41928,041,670 - 28,041,888UniSTSRGSC3.4
Celera1925,759,562 - 25,759,780UniSTS
Cytogenetic Map19q11UniSTS
RH143194  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,236,823 - 26,236,947 (+)MAPPERmRatBN7.2
Rnor_6.01929,908,144 - 29,908,267NCBIRnor6.0
Rnor_5.01940,816,686 - 40,816,809UniSTSRnor5.0
RGSC_v3.41928,041,752 - 28,041,875UniSTSRGSC3.4
Celera1925,759,644 - 25,759,767UniSTS
Cytogenetic Map19q11UniSTS
AU029195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21926,161,303 - 26,161,447 (+)MAPPERmRatBN7.2
Rnor_6.01929,833,847 - 29,833,990NCBIRnor6.0
Rnor_5.01940,744,189 - 40,744,332UniSTSRnor5.0
RGSC_v3.41927,958,518 - 27,958,661UniSTSRGSC3.4
Celera1925,685,318 - 25,685,461UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192481604133061905Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat


Genetic Models
This gene Inpp4b is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:388
Count of miRNA genes:208
Interacting mature miRNAs:253
Transcripts:ENSRNOT00000024981, ENSRNOT00000025013
Prediction methods:Microtar, 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 8 8 17 8 8 14 7 8 8
Low 3 35 44 36 2 36 3 52 35 34 3
Below cutoff 5 5 5 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC123471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U96920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U96921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000024981   ⟹   ENSRNOP00000024981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1925,925,358 - 26,280,634 (-)Ensembl
Rnor_6.0 Ensembl1929,597,905 - 29,968,424 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000025013   ⟹   ENSRNOP00000025013
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1925,925,588 - 26,280,634 (-)Ensembl
Rnor_6.0 Ensembl1929,598,280 - 29,951,493 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097624   ⟹   ENSRNOP00000085379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1925,925,588 - 26,280,634 (-)Ensembl
RefSeq Acc Id: NM_053917   ⟹   NP_446369
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,925,587 - 26,669,963 (-)NCBI
Rnor_6.01929,598,279 - 30,341,442 (-)NCBI
Rnor_5.01940,508,684 - 41,132,035 (-)NCBI
RGSC_v3.41927,722,430 - 28,363,639 (-)RGD
Celera1925,451,220 - 26,189,580 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772462   ⟹   XP_008770684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,346,238 (-)NCBI
Rnor_6.01929,598,279 - 30,008,667 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772464   ⟹   XP_008770686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,925,358 - 26,669,963 (-)NCBI
Rnor_6.01929,592,889 - 30,341,524 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601163   ⟹   XP_017456652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,925,575 - 26,670,084 (-)NCBI
Rnor_6.01929,598,279 - 30,341,527 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601164   ⟹   XP_017456653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,920,189 - 26,670,084 (-)NCBI
Rnor_6.01929,592,889 - 30,341,524 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601165   ⟹   XP_017456654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,670,085 (-)NCBI
Rnor_6.01929,598,279 - 30,341,528 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097428   ⟹   XP_038953356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,670,084 (-)NCBI
RefSeq Acc Id: XM_039097429   ⟹   XP_038953357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,589,522 (-)NCBI
RefSeq Acc Id: XM_039097430   ⟹   XP_038953358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,925,575 - 26,670,085 (-)NCBI
RefSeq Acc Id: XM_039097431   ⟹   XP_038953359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,670,085 (-)NCBI
RefSeq Acc Id: XM_039097432   ⟹   XP_038953360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,986,345 - 26,670,085 (-)NCBI
RefSeq Acc Id: XM_039097434   ⟹   XP_038953362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,164,030 (-)NCBI
RefSeq Acc Id: XM_039097435   ⟹   XP_038953363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21925,926,776 - 26,245,459 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446369   ⟸   NM_053917
- UniProtKB: Q9QWG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008770686   ⟸   XM_008772464
- Peptide Label: isoform X3
- UniProtKB: Q9QWG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008770684   ⟸   XM_008772462
- Peptide Label: isoform X1
- UniProtKB: Q9QWG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017456653   ⟸   XM_017601164
- Peptide Label: isoform X3
- UniProtKB: Q9QWG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017456654   ⟸   XM_017601165
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017456652   ⟸   XM_017601163
- Peptide Label: isoform X1
- UniProtKB: Q9QWG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024981   ⟸   ENSRNOT00000024981
RefSeq Acc Id: ENSRNOP00000025013   ⟸   ENSRNOT00000025013
RefSeq Acc Id: XP_038953358   ⟸   XM_039097430
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953359   ⟸   XM_039097431
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953356   ⟸   XM_039097428
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953357   ⟸   XM_039097429
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953363   ⟸   XM_039097435
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953362   ⟸   XM_039097434
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953360   ⟸   XM_039097432
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000085379   ⟸   ENSRNOT00000097624
Protein Domains
C2

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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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/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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: 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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
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)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620470 AgrOrtholog
Ensembl Genes ENSRNOG00000018382 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000024981 UniProtKB/Swiss-Prot
  ENSRNOP00000025013 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000024981 UniProtKB/Swiss-Prot
  ENSRNOT00000025013 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot
InterPro C2_domain_sf UniProtKB/Swiss-Prot
  INPP4 UniProtKB/Swiss-Prot
KEGG Report rno:116699 UniProtKB/Swiss-Prot
NCBI Gene 116699 ENTREZGENE
PANTHER PTHR12187 UniProtKB/Swiss-Prot
PhenoGen Inpp4b PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot
Transposagen Inpp4b Transposagen
UniProt INP4B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35825 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-12-14 Inpp4b  inositol polyphosphate-4-phosphatase, type II    inositol polyphosphate-4-phosphatase, type II, 105kD  Name updated 1299863 APPROVED
2002-08-07 Inpp4b  inositol polyphosphate-4-phosphatase, type II, 105kD      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in skeletal muscle and heart with some expression in most tissues 633135
gene_protein a 105,257-Da protein 633135