Pde7b (phosphodiesterase 7B) - Rat Genome Database

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Gene: Pde7b (phosphodiesterase 7B) Rattus norvegicus
Analyze
Symbol: Pde7b
Name: phosphodiesterase 7B
RGD ID: 621016
Description: Enables 3',5'-cyclic-AMP phosphodiesterase activity. Predicted to be involved in cAMP-mediated signaling. Orthologous to human PDE7B (phosphodiesterase 7B); PARTICIPATES IN protein kinase A (PKA) signaling pathway; purine metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cAMP-specific 3',5'-cyclic phosphodiesterase 7B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Pde7b_v2   Pde7b_v3   Pde7b_v1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2115,174,001 - 15,493,267 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl115,182,704 - 15,492,900 (-)Ensembl
Rnor_6.0115,889,845 - 16,203,909 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl115,893,533 - 16,203,909 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0117,438,266 - 17,650,404 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4115,701,127 - 15,929,632 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1115,701,194 - 15,929,679NCBI
Celera113,613,403 - 13,825,920 (-)NCBICelera
Cytogenetic Map1p12NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium dichloride  (EXP,ISO)
chloroprene  (ISO)
cisplatin  (ISO)
crocidolite asbestos  (ISO)
DDT  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dipyridamole  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
genistein  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
nickel atom  (ISO)
O-methyleugenol  (ISO)
papaverine  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorononanoic acid  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
rotenone  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
Vinpocetine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10872825   PMID:15056290   PMID:19913519  


Genomics

Comparative Map Data
Pde7b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2115,174,001 - 15,493,267 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl115,182,704 - 15,492,900 (-)Ensembl
Rnor_6.0115,889,845 - 16,203,909 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl115,893,533 - 16,203,909 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0117,438,266 - 17,650,404 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4115,701,127 - 15,929,632 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1115,701,194 - 15,929,679NCBI
Celera113,613,403 - 13,825,920 (-)NCBICelera
Cytogenetic Map1p12NCBI
PDE7B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6135,851,701 - 136,195,574 (+)EnsemblGRCh38hg38GRCh38
GRCh386135,851,701 - 136,195,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376136,172,839 - 136,516,712 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366136,214,527 - 136,558,402 (+)NCBINCBI36hg18NCBI36
Build 346136,214,526 - 136,558,402NCBI
Celera6136,913,199 - 137,257,146 (+)NCBI
Cytogenetic Map6q23.3NCBI
HuRef6133,737,120 - 134,081,400 (+)NCBIHuRef
CHM1_16136,435,326 - 136,779,229 (+)NCBICHM1_1
Pde7b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391020,272,798 - 20,600,824 (-)NCBIGRCm39mm39
GRCm39 Ensembl1020,273,750 - 20,600,824 (-)Ensembl
GRCm381020,397,052 - 20,725,078 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1020,398,004 - 20,725,078 (-)EnsemblGRCm38mm10GRCm38
MGSCv371020,117,810 - 20,444,874 (-)NCBIGRCm37mm9NCBIm37
MGSCv361020,087,420 - 20,414,494 (-)NCBImm8
Celera1020,287,078 - 20,614,904 (-)NCBICelera
Cytogenetic Map10A3NCBI
Pde7b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955439686,130 - 985,732 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955439686,197 - 985,591 (-)NCBIChiLan1.0ChiLan1.0
PDE7B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16137,707,611 - 138,049,929 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6137,707,863 - 138,047,756 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06133,615,008 - 133,960,120 (+)NCBIMhudiblu_PPA_v0panPan3
PDE7B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1128,479,641 - 28,795,644 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl128,479,968 - 28,792,008 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha129,359,759 - 29,673,797 (+)NCBI
ROS_Cfam_1.0128,635,495 - 28,950,152 (+)NCBI
UMICH_Zoey_3.1128,521,375 - 28,837,232 (+)NCBI
UNSW_CanFamBas_1.0128,406,547 - 28,720,220 (+)NCBI
UU_Cfam_GSD_1.0128,712,981 - 29,020,890 (+)NCBI
Pde7b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946123,544,020 - 123,853,873 (+)NCBI
SpeTri2.0NW_0049365603,323,264 - 3,633,083 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE7B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl127,958,270 - 28,302,412 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1127,958,261 - 28,425,754 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2131,384,842 - 31,434,768 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDE7B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11337,230,419 - 37,560,391 (-)NCBI
ChlSab1.1 Ensembl1337,226,606 - 37,378,218 (-)Ensembl
Vero_WHO_p1.0NW_0236660409,418,592 - 9,751,149 (-)NCBI
Pde7b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248861,474,076 - 1,827,608 (-)NCBI

Position Markers
D1Rat186  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,321,100 - 15,321,325 (+)MAPPERmRatBN7.2
Rnor_6.0116,033,078 - 16,033,302NCBIRnor6.0
Rnor_5.0117,574,243 - 17,574,467UniSTSRnor5.0
RGSC_v3.4115,833,442 - 15,833,667RGDRGSC3.4
RGSC_v3.4115,833,443 - 15,833,667UniSTSRGSC3.4
RGSC_v3.1115,833,505 - 15,833,729RGD
Celera113,748,791 - 13,749,015UniSTS
RH 3.4 Map1166.11RGD
RH 3.4 Map1166.11UniSTS
RH 2.0 Map183.1RGD
SHRSP x BN Map111.45RGD
Cytogenetic Map1p12UniSTS
D1Rat150  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,245,598 - 15,245,841 (+)MAPPERmRatBN7.2
Rnor_6.0115,955,566 - 15,955,808NCBIRnor6.0
Rnor_5.0117,499,606 - 17,499,848UniSTSRnor5.0
RGSC_v3.4115,786,924 - 15,787,282RGDRGSC3.4
RGSC_v3.4115,786,927 - 15,787,169UniSTSRGSC3.4
RGSC_v3.1115,786,989 - 15,787,231RGD
RH 3.4 Map1148.43RGD
RH 3.4 Map1148.43UniSTS
RH 2.0 Map177.2RGD
SHRSP x BN Map111.4099RGD
Cytogenetic Map1p12UniSTS
D1Got18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,218,672 - 15,218,826 (+)MAPPERmRatBN7.2
Rnor_6.0115,928,984 - 15,929,137NCBIRnor6.0
Rnor_5.0117,473,101 - 17,473,254UniSTSRnor5.0
RGSC_v3.4115,759,773 - 15,759,927RGDRGSC3.4
RGSC_v3.4115,759,774 - 15,759,927UniSTSRGSC3.4
RGSC_v3.1115,759,836 - 15,759,989RGD
Celera113,648,764 - 13,648,917UniSTS
RH 3.4 Map1147.61UniSTS
RH 3.4 Map1147.61RGD
RH 2.0 Map173.9RGD
Cytogenetic Map1p12UniSTS
D1Got21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,313,278 - 15,313,403 (+)MAPPERmRatBN7.2
Rnor_6.0116,025,256 - 16,025,380NCBIRnor6.0
Rnor_5.0117,566,421 - 17,566,545UniSTSRnor5.0
RGSC_v3.4115,825,620 - 15,825,745RGDRGSC3.4
RGSC_v3.4115,825,621 - 15,825,745UniSTSRGSC3.4
RGSC_v3.1115,825,683 - 15,825,807RGD
Celera113,740,969 - 13,741,093UniSTS
RH 3.4 Map1164.3UniSTS
RH 3.4 Map1164.3RGD
RH 2.0 Map184.2RGD
Cytogenetic Map1p12UniSTS
D1Got20  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,341,811 - 15,342,030 (+)MAPPERmRatBN7.2
Rnor_6.0116,053,785 - 16,054,003NCBIRnor6.0
Rnor_5.0117,594,950 - 17,595,168UniSTSRnor5.0
RGSC_v3.4115,854,109 - 15,854,399RGDRGSC3.4
RGSC_v3.4115,854,110 - 15,854,328UniSTSRGSC3.4
RGSC_v3.1115,854,172 - 15,854,390RGD
Celera113,769,427 - 13,769,645UniSTS
RH 3.4 Map1166.11RGD
RH 3.4 Map1166.11UniSTS
Cytogenetic Map1p12UniSTS
D1Ztm10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,248,417 - 15,248,567 (+)MAPPERmRatBN7.2
mRatBN7.2X30,661,961 - 30,662,016 (+)MAPPERmRatBN7.2
Rnor_6.0115,960,444 - 15,960,595NCBIRnor6.0
Rnor_5.0117,501,719 - 17,501,870UniSTSRnor5.0
Celera113,676,385 - 13,676,536UniSTS
Cytogenetic Map1p12UniSTS
D1Ztm8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,202,832 - 15,203,054 (+)MAPPERmRatBN7.2
Rnor_6.0115,913,643 - 15,913,864NCBIRnor6.0
Rnor_5.0117,458,256 - 17,458,477UniSTSRnor5.0
RGSC_v3.4115,722,312 - 15,722,533UniSTSRGSC3.4
Celera113,633,354 - 13,633,575UniSTS
Cytogenetic Map1p12UniSTS
D1Ztm9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,188,935 - 15,189,169 (+)MAPPERmRatBN7.2
Rnor_6.0115,899,765 - 15,899,998NCBIRnor6.0
Rnor_5.0117,444,498 - 17,444,731UniSTSRnor5.0
RGSC_v3.4115,707,359 - 15,707,592UniSTSRGSC3.4
Celera113,619,635 - 13,619,868UniSTS
Cytogenetic Map1p12UniSTS
BF397880  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,340,378 - 15,340,529 (+)MAPPERmRatBN7.2
Rnor_6.0116,052,352 - 16,052,502NCBIRnor6.0
Rnor_5.0117,593,517 - 17,593,667UniSTSRnor5.0
RGSC_v3.4115,852,677 - 15,852,827UniSTSRGSC3.4
Celera113,767,994 - 13,768,144UniSTS
RH 3.4 Map1166.22UniSTS
Cytogenetic Map1p12UniSTS
RH135386  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,329,499 - 15,329,683 (+)MAPPERmRatBN7.2
Rnor_6.0116,041,474 - 16,041,657NCBIRnor6.0
Rnor_5.0117,582,639 - 17,582,822UniSTSRnor5.0
RGSC_v3.4115,841,799 - 15,841,982UniSTSRGSC3.4
Celera113,757,116 - 13,757,299UniSTS
RH 3.4 Map1164.4UniSTS
Cytogenetic Map1p12UniSTS
AU049907  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2115,218,598 - 15,218,801 (+)MAPPERmRatBN7.2
Rnor_6.0115,928,910 - 15,929,112NCBIRnor6.0
Rnor_5.0117,473,027 - 17,473,229UniSTSRnor5.0
RGSC_v3.4115,759,700 - 15,759,902UniSTSRGSC3.4
Celera113,648,690 - 13,648,892UniSTS
Cytogenetic Map1p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)11532110019121980Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:101
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000018556
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 7 8 4 8 10 17 35 29 11 8
Low 3 36 47 39 15 39 1 57 12
Below cutoff 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018556   ⟹   ENSRNOP00000018556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl115,182,704 - 15,492,830 (-)Ensembl
Rnor_6.0 Ensembl115,893,533 - 16,203,838 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078586   ⟹   ENSRNOP00000070401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl115,182,704 - 15,492,900 (-)Ensembl
Rnor_6.0 Ensembl115,893,533 - 16,203,909 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101303   ⟹   ENSRNOP00000094058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl115,182,704 - 15,397,916 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113170   ⟹   ENSRNOP00000083905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl115,182,704 - 15,336,818 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117741   ⟹   ENSRNOP00000088274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl115,182,704 - 15,292,530 (-)Ensembl
RefSeq Acc Id: NM_080894   ⟹   NP_543170
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,182,704 - 15,492,900 (-)NCBI
Rnor_6.0115,893,533 - 16,203,909 (-)NCBI
Rnor_5.0117,438,266 - 17,650,404 (-)NCBI
RGSC_v3.4115,701,127 - 15,929,632 (-)RGD
Celera113,613,403 - 13,825,920 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758591   ⟹   XP_008756813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,179,711 - 15,332,491 (-)NCBI
Rnor_6.0115,889,845 - 16,041,143 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758592   ⟹   XP_008756814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,179,711 - 15,263,151 (-)NCBI
Rnor_6.0115,889,845 - 15,975,193 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082826   ⟹   XP_038938754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,174,001 - 15,332,499 (-)NCBI
RefSeq Acc Id: XM_039082864   ⟹   XP_038938792
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,179,711 - 15,493,267 (-)NCBI
RefSeq Acc Id: XM_039082890   ⟹   XP_038938818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,179,711 - 15,263,752 (-)NCBI
RefSeq Acc Id: XR_005488707
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2115,174,263 - 15,332,499 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_543170   ⟸   NM_080894
- UniProtKB: Q8VIE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008756813   ⟸   XM_008758591
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756814   ⟸   XM_008758592
- Peptide Label: isoform X4
- UniProtKB: Q8VIE3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018556   ⟸   ENSRNOT00000018556
RefSeq Acc Id: ENSRNOP00000070401   ⟸   ENSRNOT00000078586
RefSeq Acc Id: XP_038938754   ⟸   XM_039082826
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038938792   ⟸   XM_039082864
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938818   ⟸   XM_039082890
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000088274   ⟸   ENSRNOT00000117741
RefSeq Acc Id: ENSRNOP00000083905   ⟸   ENSRNOT00000113170
RefSeq Acc Id: ENSRNOP00000094058   ⟸   ENSRNOT00000101303
Protein Domains
PDEase

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)
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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)
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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)
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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-Lx/CubMcwi (2019)
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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)
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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)
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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)
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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)
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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 (2020)
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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)
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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)
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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)
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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)
DA/OlaHsd (2019)
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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)
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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)
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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)
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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)
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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
F344/Stm (2019)
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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)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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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)
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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)
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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/FarMcwi (2019)
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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)
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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
HXB10/IpcvMcwi (2019)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
LEXF10A/StmMcwi (2020)
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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)
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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)
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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)
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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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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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)
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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)
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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)
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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)
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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)
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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
SHR/OlalpcvMcwi (2019)
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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)
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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)
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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 (2020)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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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)
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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 (2020)
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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)
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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 (2019)
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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)
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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 (2020)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621016 AgrOrtholog
Ensembl Genes ENSRNOG00000013436 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018556 UniProtKB/TrEMBL
  ENSRNOP00000070401 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018556 UniProtKB/TrEMBL
  ENSRNOT00000078586 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.1300.10 UniProtKB/TrEMBL
InterPro Metal-dep_PHydrolase_HD_dom UniProtKB/TrEMBL
  PDEase UniProtKB/TrEMBL
  PDEase_catalytic_dom UniProtKB/TrEMBL
  PDEase_catalytic_dom_sf UniProtKB/TrEMBL
  PDEase_CS UniProtKB/TrEMBL
KEGG Report rno:140929 UniProtKB/TrEMBL
NCBI Gene 140929 ENTREZGENE
Pfam PDEase_I UniProtKB/TrEMBL
PhenoGen Pde7b PhenoGen
PRINTS PDIESTERASE1 UniProtKB/TrEMBL
PROSITE PDEASE_I UniProtKB/TrEMBL
  PDEASE_I_2 UniProtKB/TrEMBL
SMART HDc UniProtKB/TrEMBL
UniProt Q8VIE2_RAT UniProtKB/TrEMBL
  Q8VIE3 ENTREZGENE, UniProtKB/TrEMBL
  Q8VIE4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LN39 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pde7b  phosphodiesterase 7B      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pde7b  phosphodiesterase 7B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in the striatum and testis 625534