Pde4d (phosphodiesterase 4D) - Rat Genome Database

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Gene: Pde4d (phosphodiesterase 4D) Rattus norvegicus
Analyze
Symbol: Pde4d
Name: phosphodiesterase 4D
RGD ID: 3281
Description: Enables beta-2 adrenergic receptor binding activity; cyclic-nucleotide phosphodiesterase activity; and enzyme binding activity. Involved in several processes, including positive regulation of smooth muscle cell migration; positive regulation of smooth muscle cell proliferation; and regulation of signal transduction. Located in several cellular components, including Golgi apparatus; centrosome; and myofibril. Part of protein-containing complex. Used to study mental depression. Biomarker of transient cerebral ischemia. Human ortholog(s) of this gene implicated in acrodysostosis. Orthologous to human PDE4D (phosphodiesterase 4D); PARTICIPATES IN protein kinase A (PKA) signaling pathway; adenine phoshoribosyltransferase deficiency pathway; adenosine monophosphate deaminase deficiency pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 3',5'-cyclic AMP phosphodiesterase; cAMP-specific 3',5'-cyclic phosphodiesterase 4D; cAMP-specific phosphodiesterase PDE4D; cAMP-specific phosphodiesterase splice variant PDE4D8; DPDE3; PDE3/IVd; Phosphodiesterase 4D cAMP-specific (dunce; Phosphodiesterase 4D cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3); phosphodiesterase 4D, cAMP specific; Phosphodiesterase 4D, cAMP-specific (dunce; phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: Pde4dTn(sb-T2/Bart3)2.285Mcwi  
Genetic Models: F344-Pde4dTn(sb-T2/Bart3)2.285Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2240,014,933 - 41,529,190 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl240,554,146 - 41,464,264 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0240,219,999 - 41,468,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0259,292,847 - 59,860,049 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0260,035,104 - 60,521,358 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4240,196,097 - 41,311,012 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1241,035,303 - 41,231,381NCBI
Celera236,258,764 - 37,353,786 (+)NCBICelera
Cytogenetic Map2q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrobenzenesulfonic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(hydroxymethyl)cytosine  (ISO)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
diarsenic trioxide  (ISO)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (EXP)
fluoxetine  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
leflunomide  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
mitoxantrone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
ozone  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
picrotoxin  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
raloxifene  (ISO)
rifampicin  (ISO)
roflumilast  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
temozolomide  (ISO)
testosterone enanthate  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
torcetrapib  (ISO)
tributylstannane  (EXP)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adenylate cyclase-activating adrenergic receptor signaling pathway involved in positive regulation of heart rate  (IC)
adrenergic receptor signaling pathway  (IMP)
aging  (ISO)
cAMP catabolic process  (IBA,IEA,ISO)
cellular protein-containing complex assembly  (IDA)
cellular response to cAMP  (ISO)
cellular response to epinephrine stimulus  (ISO)
cellular response to lipopolysaccharide  (ISO)
establishment of endothelial barrier  (IDA)
leukocyte migration  (ISO)
lung development  (IEP)
memory  (IEP,IMP)
multicellular organism growth  (ISO)
negative regulation of cAMP-mediated signaling  (IBA,IEA,ISO)
negative regulation of heart contraction  (ISO)
negative regulation of peptidyl-serine phosphorylation  (ISO)
negative regulation of relaxation of cardiac muscle  (ISO)
neutrophil chemotaxis  (ISO)
positive regulation of cell-cell adhesion  (IMP)
positive regulation of interferon-gamma production  (IEA,ISO)
positive regulation of interleukin-2 production  (IEA,ISO)
positive regulation of interleukin-5 production  (IEA,ISO)
positive regulation of protein phosphorylation  (IDA)
positive regulation of smooth muscle cell migration  (IMP)
positive regulation of smooth muscle cell proliferation  (IMP)
regulation of cAMP-mediated signaling  (IMP)
regulation of cardiac muscle cell contraction  (IBA,IMP,ISO)
regulation of G protein-coupled receptor signaling pathway  (IDA)
regulation of heart rate  (ISO)
regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (ISO)
regulation of ryanodine-sensitive calcium-release channel activity  (ISO)
regulation of signaling receptor activity  (IMP)
signal transduction  (IBA)
smooth muscle contraction  (ISO)
T cell receptor signaling pathway  (IEA,ISO)

Cellular Component

References

References - curated
1. Acin-Perez R, etal., J Biol Chem. 2011 Sep 2;286(35):30423-32. doi: 10.1074/jbc.M111.266379. Epub 2011 Jul 1.
2. Baillie GS, etal., Proc Natl Acad Sci U S A 2003 Feb 4;100(3):940-5.
3. Bevan S, etal., Stroke. 2005 May;36(5):949-53. Epub 2005 Mar 31.
4. Bolger GB, etal., Gene 1994 Nov 18;149(2):237-44.
5. Boone M and Deen PM, Pflugers Arch. 2008 Sep;456(6):1005-24. Epub 2008 Apr 23.
6. Brophy VH, etal., Stroke. 2006 Jun;37(6):1385-90. Epub 2006 May 4.
7. Bruno O, etal., Br J Pharmacol. 2011 Dec;164(8):2054-63. doi: 10.1111/j.1476-5381.2011.01524.x.
8. Conti M and Beavo J, Annu Rev Biochem. 2007;76:481-511.
9. Creighton J, etal., J Cell Sci. 2008 Jan 1;121(Pt 1):110-9. Epub 2007 Dec 11.
10. De Arcangelis V, etal., J Biol Chem. 2009 Dec 4;284(49):33824-32. doi: 10.1074/jbc.M109.020388. Epub 2009 Oct 1.
11. Dodge KL, etal., EMBO J 2001 Apr 17;20(8):1921-30.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Giorgi M, etal., Behav Brain Res. 2004 Sep 23;154(1):99-106.
14. GOA data from the GO Consortium
15. Gretarsdottir S, etal., Nat Genet. 2003 Oct;35(2):131-8. Epub 2003 Sep 21.
16. He Z, etal., ACS Chem Neurosci. 2012 Jun 20;3(6):428-32. doi: 10.1021/cn2001156. Epub 2012 Feb 27.
17. Huo Z, etal., Biochem Biophys Res Commun. 2012 Oct 12;427(1):73-9. doi: 10.1016/j.bbrc.2012.09.005. Epub 2012 Sep 10.
18. KEGG
19. Lee JH, etal., J Biol Chem. 2007 Apr 6;282(14):10414-22. Epub 2007 Jan 23.
20. Liu L, etal., Stroke Res Treat. 2011;2011:534257. doi: 10.4061/2011/534257. Epub 2011 Jun 9.
21. Lopez E, etal., Dev Dyn. 2010 Sep;239(9):2470-8. doi: 10.1002/dvdy.22374.
22. McSorley T, etal., Eur J Cell Biol. 2006 Jul;85(7):673-8. Epub 2006 Feb 28.
23. MGD data from the GO Consortium
24. Miro X, etal., Synapse 2002 Sep 15;45(4):259-69.
25. Monaco L, etal., J Biol Chem 1994 Jan 7;269(1):347-57.
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Oliva AA Jr, etal., J Neurochem. 2012 Dec;123(6):1019-29. doi: 10.1111/jnc.12049. Epub 2012 Nov 1.
28. OMIM Disease Annotation Pipeline
29. Paruthiyil S, etal., Proc Natl Acad Sci U S A 2002 Dec 24;99(26):17191-6.
30. Pipeline to import KEGG annotations from KEGG into RGD
31. Pipeline to import SMPDB annotations from SMPDB into RGD
32. RGD automated data pipeline
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Richter W, etal., Biochem J. 2005 Jun 15;388(Pt 3):803-11.
36. Richter W, etal., EMBO Rep. 2013 Mar 1;14(3):276-83. doi: 10.1038/embor.2013.4. Epub 2013 Feb 5.
37. Schaefer TL, etal., Genes Brain Behav. 2012 Jul;11(5):614-22. doi: 10.1111/j.1601-183X.2012.00796.x. Epub 2012 May 8.
38. Sette C, etal., J Biol Chem 1994 Jul 15;269(28):18271-4.
39. Staton JM, etal., J Neurol Neurosurg Psychiatry. 2006 Sep;77(9):1067-9.
40. Swinnen JV, etal., J Biol Chem 1991 Sep 25;266(27):18370-7.
41. Swinnen JV, etal., Proc Natl Acad Sci U S A 1989 Jul;86(14):5325-9.
42. Swinnen JV, etal., Proc Natl Acad Sci U S A 1989 Nov;86(21):8197-201.
43. Tasken KA, etal., J Biol Chem. 2001 Jun 22;276(25):21999-2002. Epub 2001 Apr 2.
44. Tilley DG and Maurice DH, Mol Pharmacol. 2002 Sep;62(3):497-506.
45. Verde I, etal., J Biol Chem 2001 Apr 6;276(14):11189-98. Epub 2000 Dec 27.
46. Wang D, etal., Cell Signal 2003 Sep;15(9):883-91.
47. Wang J, etal., Am J Physiol Heart Circ Physiol. 2010 Apr;298(4):H1146-54. doi: 10.1152/ajpheart.00252.2009. Epub 2010 Feb 5.
48. Xu XW, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2007 Oct;24(5):491-4.
49. Zee RY, etal., Stroke. 2006 Aug;37(8):2012-7. Epub 2006 Jul 6.
Additional References at PubMed
PMID:8413254   PMID:9371713   PMID:10187850   PMID:10518565   PMID:10571082   PMID:12121997   PMID:14519662   PMID:15182229   PMID:15585880   PMID:15938621   PMID:16213210   PMID:17261351  
PMID:17404263   PMID:18983980   PMID:19060129   PMID:19252089   PMID:20106966   PMID:20302880   PMID:20819076   PMID:21670503   PMID:21903937   PMID:23887098   PMID:24815749   PMID:25064455  
PMID:25918234   PMID:25931508   PMID:27923787   PMID:28339772   PMID:30053369   PMID:30628641   PMID:32212953  


Genomics

Comparative Map Data
Pde4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2240,014,933 - 41,529,190 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl240,554,146 - 41,464,264 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0240,219,999 - 41,468,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0259,292,847 - 59,860,049 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0260,035,104 - 60,521,358 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4240,196,097 - 41,311,012 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1241,035,303 - 41,231,381NCBI
Celera236,258,764 - 37,353,786 (+)NCBICelera
Cytogenetic Map2q14NCBI
PDE4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl558,969,038 - 60,522,120 (-)EnsemblGRCh38hg38GRCh38
GRCh38558,969,038 - 60,524,329 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37558,264,865 - 59,792,113 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36558,300,622 - 59,225,378 (-)NCBINCBI36hg18NCBI36
Build 34558,302,467 - 58,918,032NCBI
Celera555,205,298 - 56,725,032 (-)NCBI
Cytogenetic Map5q11.2-q12.1NCBI
HuRef555,222,770 - 56,741,723 (-)ENTREZGENEHuRef
CHM1_1558,265,111 - 59,783,530 (-)NCBICHM1_1
Pde4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913108,790,711 - 110,092,503 (+)NCBIGRCm39mm39
GRCm39 Ensembl13108,586,482 - 110,089,995 (+)Ensembl
GRCm3813108,654,177 - 109,955,969 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13108,449,948 - 109,953,461 (+)EnsemblGRCm38mm10GRCm38
MGSCv3713109,444,371 - 110,741,682 (+)NCBIGRCm37mm9NCBIm37
MGSCv3613109,775,041 - 111,072,352 (+)NCBImm8
Celera13112,976,414 - 114,285,878 (+)NCBICelera
Cytogenetic Map13D2.1NCBI
cM Map1359.69NCBI
Pde4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554468,211,877 - 9,252,653 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554467,914,326 - 9,252,527 (+)NCBIChiLan1.0ChiLan1.0
PDE4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1555,749,248 - 56,675,724 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl555,749,214 - 56,670,111 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0553,510,287 - 55,039,181 (+)NCBIMhudiblu_PPA_v0panPan3
PDE4D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1245,843,767 - 47,245,263 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl245,846,294 - 46,949,912 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha242,920,230 - 44,321,074 (-)NCBI
ROS_Cfam_1.0246,331,498 - 47,722,409 (-)NCBI
UMICH_Zoey_3.1243,375,010 - 44,793,218 (-)NCBI
UNSW_CanFamBas_1.0244,204,482 - 45,049,239 (-)NCBI
UU_Cfam_GSD_1.0245,031,308 - 46,431,653 (-)NCBI
Pde4d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213199,501,304 - 200,299,009 (+)NCBI
SpeTri2.0NW_0049364808,123,437 - 9,235,586 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDE4D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1637,897,300 - 39,154,586 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11637,897,300 - 39,406,534 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21640,637,293 - 40,680,968 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103221883
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1455,148,012 - 56,665,684 (-)NCBI
ChlSab1.1 Ensembl455,153,563 - 55,390,027 (-)Ensembl
Vero_WHO_p1.0NW_0236660494,132,259 - 4,425,088 (-)NCBI

Position Markers
D2Rat18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,125,789 - 41,125,954 (+)MAPPERmRatBN7.2
Rnor_6.0241,063,439 - 41,063,603NCBIRnor6.0
Rnor_5.0260,126,669 - 60,126,833UniSTSRnor5.0
RGSC_v3.4240,912,197 - 40,912,362RGDRGSC3.4
RGSC_v3.4240,912,198 - 40,912,362UniSTSRGSC3.4
RGSC_v3.1240,832,566 - 40,832,731RGD
Celera236,959,987 - 36,960,151UniSTS
RH 3.4 Map2178.9RGD
RH 3.4 Map2178.9UniSTS
RH 2.0 Map251.8RGD
SHRSP x BN Map218.4498RGD
Cytogenetic Map2q16UniSTS
D2Rat199  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,243,963 - 41,244,106 (+)MAPPERmRatBN7.2
Rnor_6.0241,179,255 - 41,179,397NCBIRnor6.0
Rnor_5.0260,242,455 - 60,242,597UniSTSRnor5.0
RGSC_v3.4241,032,071 - 41,032,214RGDRGSC3.4
RGSC_v3.4241,032,072 - 41,032,214UniSTSRGSC3.4
RGSC_v3.1240,952,440 - 40,952,583RGD
Celera237,077,901 - 37,078,043UniSTS
SHRSP x BN Map218.4498RGD
SHRSP x BN Map218.4498UniSTS
Cytogenetic Map2q16UniSTS
D2Got25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,436,472 - 41,436,590 (+)MAPPERmRatBN7.2
Rnor_6.0241,377,297 - 41,377,414NCBIRnor6.0
Rnor_5.0260,435,279 - 60,435,396UniSTSRnor5.0
RGSC_v3.4241,230,728 - 41,230,846RGDRGSC3.4
RGSC_v3.4241,230,729 - 41,230,846UniSTSRGSC3.4
RGSC_v3.1241,151,098 - 41,151,215RGD
Celera237,265,313 - 37,265,430UniSTS
RH 3.4 Map2182.08RGD
RH 3.4 Map2182.08UniSTS
Cytogenetic Map2q16UniSTS
D2Rat317  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,150,068 - 41,150,174 (+)MAPPERmRatBN7.2
Rnor_6.0241,088,291 - 41,088,396NCBIRnor6.0
Rnor_5.0260,151,521 - 60,151,626UniSTSRnor5.0
RGSC_v3.4240,937,068 - 40,937,174RGDRGSC3.4
RGSC_v3.4240,937,069 - 40,937,174UniSTSRGSC3.4
RGSC_v3.1240,857,437 - 40,857,543RGD
Celera236,984,267 - 36,984,386UniSTS
Cytogenetic Map2q16UniSTS
D2Mco27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2240,986,607 - 40,986,991 (+)MAPPERmRatBN7.2
mRatBN7.2240,986,776 - 40,986,991 (+)MAPPERmRatBN7.2
Rnor_6.0240,924,434 - 40,924,648NCBIRnor6.0
Rnor_6.0240,924,265 - 40,924,648NCBIRnor6.0
Rnor_5.0259,987,339 - 59,987,722UniSTSRnor5.0
Rnor_5.0259,987,508 - 59,987,722UniSTSRnor5.0
RGSC_v3.4240,772,231 - 40,772,445UniSTSRGSC3.4
RGSC_v3.4240,772,230 - 40,772,445RGDRGSC3.4
RGSC_v3.4240,772,062 - 40,772,445UniSTSRGSC3.4
RGSC_v3.1240,692,599 - 40,692,814RGD
Celera236,820,729 - 36,820,943UniSTS
Celera236,820,560 - 36,820,943UniSTS
Cytogenetic Map2q16UniSTS
AU049525  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,449,730 - 41,449,926 (+)MAPPERmRatBN7.2
Rnor_6.0241,390,554 - 41,390,749NCBIRnor6.0
Rnor_6.0241,364,009 - 41,364,204NCBIRnor6.0
Rnor_5.0260,422,531 - 60,422,726UniSTSRnor5.0
Rnor_5.0260,448,536 - 60,448,731UniSTSRnor5.0
RGSC_v3.4241,244,258 - 41,244,453UniSTSRGSC3.4
Celera237,278,568 - 37,278,754UniSTS
Cytogenetic Map2q16UniSTS
13.MMHAP86FRE7.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,141,186 - 41,141,371 (+)MAPPERmRatBN7.2
Rnor_6.0241,078,833 - 41,079,017NCBIRnor6.0
Rnor_5.0260,142,063 - 60,142,247UniSTSRnor5.0
RGSC_v3.4240,928,182 - 40,928,366UniSTSRGSC3.4
Celera236,975,374 - 36,975,558UniSTS
Cytogenetic Map2q16UniSTS
BF403774  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2240,798,017 - 40,798,237 (+)MAPPERmRatBN7.2
Rnor_6.0240,729,763 - 40,729,982NCBIRnor6.0
Rnor_5.0259,798,939 - 59,799,158UniSTSRnor5.0
RGSC_v3.4240,573,177 - 40,573,396UniSTSRGSC3.4
Celera236,627,696 - 36,627,915UniSTS
RH 3.4 Map2179.5UniSTS
Cytogenetic Map2q16UniSTS
AA955553  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2239,858,384 - 39,858,570 (-)MAPPERmRatBN7.2
Rnor_6.0240,371,486 - 40,371,671NCBIRnor6.0
Rnor_5.0259,444,339 - 59,444,524UniSTSRnor5.0
RGSC_v3.4239,597,595 - 39,597,780UniSTSRGSC3.4
Celera235,698,523 - 35,698,708UniSTS
RH 3.4 Map2169.5UniSTS
Cytogenetic Map2q16UniSTS
AU046382  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2240,629,377 - 40,629,570 (+)MAPPERmRatBN7.2
Rnor_6.0240,557,963 - 40,558,155NCBIRnor6.0
Rnor_5.0259,630,646 - 59,630,838UniSTSRnor5.0
RGSC_v3.4240,398,091 - 40,398,283UniSTSRGSC3.4
Celera236,459,293 - 36,459,485UniSTS
Cytogenetic Map2q16UniSTS
RH138883  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,230,167 - 41,230,319 (+)MAPPERmRatBN7.2
Rnor_6.0241,165,464 - 41,165,615NCBIRnor6.0
Rnor_5.0260,228,664 - 60,228,815UniSTSRnor5.0
RGSC_v3.4241,018,282 - 41,018,433UniSTSRGSC3.4
Celera237,064,295 - 37,064,446UniSTS
RH 3.4 Map2180.69UniSTS
Cytogenetic Map2q16UniSTS
BF401594  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,331,465 - 41,331,682 (+)MAPPERmRatBN7.2
Rnor_6.0241,267,117 - 41,267,333NCBIRnor6.0
Rnor_5.0260,330,317 - 60,330,533UniSTSRnor5.0
RGSC_v3.4241,120,213 - 41,120,429UniSTSRGSC3.4
Celera237,165,717 - 37,165,933UniSTS
RH 3.4 Map2169.9UniSTS
Cytogenetic Map2q16UniSTS
BQ192875  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,356,850 - 41,357,038 (+)MAPPERmRatBN7.2
Rnor_6.0241,292,663 - 41,292,850NCBIRnor6.0
Rnor_5.0260,355,729 - 60,355,916UniSTSRnor5.0
RGSC_v3.4241,145,614 - 41,145,801UniSTSRGSC3.4
Celera237,191,179 - 37,191,366UniSTS
RH 3.4 Map2168.7UniSTS
Cytogenetic Map2q16UniSTS
fb98c02.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2241,144,489 - 41,145,581 (+)MAPPERmRatBN7.2
Rnor_6.0241,082,136 - 41,083,227NCBIRnor6.0
Rnor_5.0260,145,366 - 60,146,457UniSTSRnor5.0
Cytogenetic Map2q16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
731179Mamtr3Mammary tumor resistance QTL 30.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)23237377043665178Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
12879863Bp402Blood pressure QTL 4020.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24112578956532139Rat


Genetic Models
This gene Pde4d is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:170
Count of miRNA genes:99
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000015138, ENSRNOT00000066384, ENSRNOT00000067546, ENSRNOT00000073231, ENSRNOT00000073552
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 34 18 10 18 10 8 10 64 11 7 8 8
Low 3 9 39 31 1 31 1 10 24 34 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001113328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001113329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001113332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001113334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760721 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101737 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF031373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF536974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF536979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH000839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY388961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ266362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF102484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF121818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L27059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L27060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U09457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000015138   ⟹   ENSRNOP00000015138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl240,554,146 - 41,464,064 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000066384   ⟹   ENSRNOP00000063446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl241,157,823 - 41,464,264 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067546   ⟹   ENSRNOP00000062384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl241,442,241 - 41,464,088 (+)Ensembl
RefSeq Acc Id: NM_001113328   ⟹   NP_001106799
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,723,169 - 41,524,760 (+)NCBI
Rnor_6.0240,655,399 - 41,464,118 (+)NCBI
Rnor_5.0259,292,847 - 59,860,049 (+)NCBI
Rnor_5.0260,035,104 - 60,521,358 (+)NCBI
RGSC_v3.4240,196,097 - 41,311,012 (+)RGD
Celera236,553,176 - 37,353,786 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001113329   ⟹   NP_001106800
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,428,088 - 41,524,760 (+)NCBI
Rnor_6.0240,219,999 - 41,464,118 (+)NCBI
Rnor_5.0259,292,847 - 59,860,049 (+)NCBI
Rnor_5.0260,035,104 - 60,521,358 (+)NCBI
RGSC_v3.4240,196,097 - 41,311,012 (+)RGD
Celera236,258,764 - 37,353,786 (+)RGD
Sequence:
RefSeq Acc Id: NM_001113332   ⟹   NP_001106803
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,859,364 - 41,524,760 (+)NCBI
Rnor_6.0240,792,669 - 41,464,118 (+)NCBI
Rnor_5.0259,292,847 - 59,860,049 (+)NCBI
Rnor_5.0260,035,104 - 60,521,358 (+)NCBI
RGSC_v3.4240,196,097 - 41,311,012 (+)RGD
Celera236,694,602 - 37,353,786 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001113334   ⟹   NP_001106805
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,222,686 - 41,524,760 (+)NCBI
Rnor_6.0241,157,982 - 41,464,118 (+)NCBI
Rnor_5.0260,035,104 - 60,521,358 (+)NCBI
RGSC_v3.4240,196,097 - 41,311,012 (+)RGD
Celera237,056,813 - 37,353,786 (+)NCBI
Sequence:
RefSeq Acc Id: NM_017032   ⟹   NP_058728
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,034,225 - 41,524,760 (+)NCBI
Rnor_6.0240,971,874 - 41,464,118 (+)NCBI
Rnor_5.0260,035,104 - 60,521,358 (+)NCBI
RGSC_v3.4240,196,097 - 41,311,012 (+)RGD
Celera236,868,159 - 37,353,786 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760721   ⟹   XP_008758943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,273,333 - 41,529,190 (+)NCBI
Rnor_6.0241,209,908 - 41,468,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760722   ⟹   XP_008758944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,501,259 - 41,529,190 (+)NCBI
Rnor_6.0241,434,127 - 41,468,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760723   ⟹   XP_008758945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,478,964 - 41,529,190 (+)NCBI
Rnor_6.0241,418,351 - 41,468,551 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101733   ⟹   XP_038957661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,014,933 - 41,529,190 (+)NCBI
RefSeq Acc Id: XM_039101734   ⟹   XP_038957662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,014,933 - 41,529,190 (+)NCBI
RefSeq Acc Id: XM_039101735   ⟹   XP_038957663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2240,196,908 - 41,529,190 (+)NCBI
RefSeq Acc Id: XM_039101736   ⟹   XP_038957664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,170,622 - 41,529,190 (+)NCBI
RefSeq Acc Id: XM_039101737   ⟹   XP_038957665
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,487,590 - 41,529,190 (+)NCBI
RefSeq Acc Id: XM_039101739   ⟹   XP_038957667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2241,498,378 - 41,529,190 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001106799 (Get FASTA)   NCBI Sequence Viewer  
  NP_001106800 (Get FASTA)   NCBI Sequence Viewer  
  NP_001106803 (Get FASTA)   NCBI Sequence Viewer  
  NP_001106805 (Get FASTA)   NCBI Sequence Viewer  
  NP_058728 (Get FASTA)   NCBI Sequence Viewer  
  XP_008758943 (Get FASTA)   NCBI Sequence Viewer  
  XP_008758944 (Get FASTA)   NCBI Sequence Viewer  
  XP_008758945 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957661 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957662 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957663 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957664 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957665 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957667 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA18924 (Get FASTA)   NCBI Sequence Viewer  
  AAA18925 (Get FASTA)   NCBI Sequence Viewer  
  AAA20393 (Get FASTA)   NCBI Sequence Viewer  
  AAA20401 (Get FASTA)   NCBI Sequence Viewer  
  AAA56857 (Get FASTA)   NCBI Sequence Viewer  
  AAB81869 (Get FASTA)   NCBI Sequence Viewer  
  AAB95266 (Get FASTA)   NCBI Sequence Viewer  
  AAC26969 (Get FASTA)   NCBI Sequence Viewer  
  AAN10116 (Get FASTA)   NCBI Sequence Viewer  
  AAN10121 (Get FASTA)   NCBI Sequence Viewer  
  AAQ90405 (Get FASTA)   NCBI Sequence Viewer  
  ABK97408 (Get FASTA)   NCBI Sequence Viewer  
  ABL14108 (Get FASTA)   NCBI Sequence Viewer  
  EDM10316 (Get FASTA)   NCBI Sequence Viewer  
  EDM10319 (Get FASTA)   NCBI Sequence Viewer  
  EDM10322 (Get FASTA)   NCBI Sequence Viewer  
  EDM10323 (Get FASTA)   NCBI Sequence Viewer  
  EDM10325 (Get FASTA)   NCBI Sequence Viewer  
  EDM10327 (Get FASTA)   NCBI Sequence Viewer  
  P14270 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058728   ⟸   NM_017032
- Peptide Label: isoform 5
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001106800   ⟸   NM_001113329
- Peptide Label: isoform 2
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001106799   ⟸   NM_001113328
- Peptide Label: isoform 1
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001106803   ⟸   NM_001113332
- Peptide Label: isoform 3
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001106805   ⟸   NM_001113334
- Peptide Label: isoform 4
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008758943   ⟸   XM_008760721
- Peptide Label: isoform X3
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008758945   ⟸   XM_008760723
- Peptide Label: isoform X6
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008758944   ⟸   XM_008760722
- Peptide Label: isoform X5
- UniProtKB: P14270 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062384   ⟸   ENSRNOT00000067546
RefSeq Acc Id: ENSRNOP00000063446   ⟸   ENSRNOT00000066384
RefSeq Acc Id: ENSRNOP00000015138   ⟸   ENSRNOT00000015138
RefSeq Acc Id: XP_038957661   ⟸   XM_039101733
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957662   ⟸   XM_039101734
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957663   ⟸   XM_039101735
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957664   ⟸   XM_039101736
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957665   ⟸   XM_039101737
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957667   ⟸   XM_039101739
- Peptide Label: isoform X7
Protein Domains
PDEase

Transcriptome

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

Promoters
RGD ID:13691132
Promoter ID:EPDNEW_R1656
Type:multiple initiation site
Name:Pde4d_1
Description:phosphodiesterase 4D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0241,157,840 - 41,157,900EPDNEW

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)
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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)
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)
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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)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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:3281 AgrOrtholog
Ensembl Genes ENSRNOG00000042536 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015138 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000062384 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000063446 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015138 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000066384 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000067546 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.1300.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HD/PDEase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDE4_UCR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_catalytic_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24627 UniProtKB/Swiss-Prot
NCBI Gene 24627 ENTREZGENE
Pfam PDE4_UCR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEase_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PDE4D RGD
PhenoGen Pde4d PhenoGen
PRINTS PDIESTERASE1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PDEASE_I_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDEASE_I_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Transposagen Pde4d Transposagen
UniProt A0A140TAB1_RAT UniProtKB/TrEMBL
  P14270 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A1E347 UniProtKB/Swiss-Prot
  A1EC59 UniProtKB/Swiss-Prot
  F1M1H7 UniProtKB/Swiss-Prot
  O35470 UniProtKB/Swiss-Prot
  Q6TRI0 UniProtKB/Swiss-Prot
  Q8CG04 UniProtKB/Swiss-Prot
  Q8CG06 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-08-29 Pde4d  phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)  Pde4d  phosphodiesterase 4D, cAMP specific  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Pde4d  phosphodiesterase 4D, cAMP specific    phosphodiesterase 4D  Name updated 1299863 APPROVED
2002-06-10 Pde4d  Phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction protein froms a complex with Adrb2 following isoprenaline treatment of cardiac myocytes 629543
gene_process involved in the activation of Mapk1 and Mapk3 629543
gene_process targeted expression to Gnrh1 neurons in transgenic rats inhibited the preovulatory luteinizing hormone (LH) surge in cycling females and the pulsatile release of LH in castrated males and females 629543