Cyp2d4 (cytochrome P450, family 2, subfamily d, polypeptide 4) - Rat Genome Database

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Gene: Cyp2d4 (cytochrome P450, family 2, subfamily d, polypeptide 4) Rattus norvegicus
Analyze
Symbol: Cyp2d4
Name: cytochrome P450, family 2, subfamily d, polypeptide 4
RGD ID: 620640
Description: Enables arachidonic acid monooxygenase activity. Involved in several processes, including C21-steroid hormone metabolic process; arachidonic acid metabolic process; and phenol-containing compound biosynthetic process. Located in intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in acute lymphoblastic leukemia; acute myeloid leukemia; asthma; autoimmune hepatitis; and rhinitis. Orthologous to several human genes including CYP2D6 (cytochrome P450 family 2 subfamily D member 6); PARTICIPATES IN celecoxib pharmacodynamics pathway; celecoxib pharmacokinetics pathway; citalopram pharmacodynamics pathway; INTERACTS WITH (S)-duloxetine hydrochloride; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cyp2d18; Cyp2d22; Cyp2d4v1; Cyp2d4v2; Cyp2d6; Cyp2d6_mapped; CYPIID18; CYPIID4; cytochrome P450 2D-29; cytochrome P450 2D-35; cytochrome P450 2D18; cytochrome P450 2D4; Cytochrome P450 subfamily IID4; cytochrome P450, family 2, subfamily d, polypeptide 22; cytochrome P450, subfamily 2D, polypeptide 6; Cytochrome P450, subfamily IID, polypeptide 6; cytochrome P450, subfamily IID, polypeptide 6 (mapped); Cytochrome P450, subfamily IID4; cytochrome P450-CMF3; cytochrome P450-DB4; debrisoquine 4-hydroxylase; P450 2D-29/2D-35; P450-CMF3; P450-DB4
RGD Orthologs
Human
Mouse
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,882,584 - 113,891,754 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,881,618 - 113,891,759 (-)Ensembl
Rnor_6.07123,599,264 - 123,608,436 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,599,266 - 123,608,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,583,983 - 123,593,008 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,742,273 - 120,752,274 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,775,536 - 120,786,502 (-)NCBI
Celera7110,197,422 - 110,206,650 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(E,E)-germacrone  (ISO)
(R)-lipoic acid  (ISO)
(R,R)-tramadol  (ISO)
(S)-duloxetine hydrochloride  (EXP)
(S)-nicotine  (ISO)
(S)-timolol (anhydrous)  (ISO)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (ISO)
1,4-naphthoquinone  (ISO)
1-(3-chlorophenyl)piperazine  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthol  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
3,4-Methylenedioxyamphetamine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,5-xylenol  (ISO)
3-methylcholanthrene  (EXP)
3-methylthiopropanal  (ISO)
4'-hydroxydiclofenac  (ISO)
4'-hydroxypropanolol  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (EXP)
4-(methylsulfinyl)phenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-Hydroxy-N-desmethyltamoxifen  (ISO)
4-Hydroxyclonidine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-Ipomeanol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-hydroxydiclofenac  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP,ISO)
5-methoxy-N,N-diisopropyltryptamine  (ISO)
5-methoxyindole  (ISO)
5-methoxytryptamine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
8-hydroxy-2'-deoxyguanosine  (ISO)
aconitine  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
ajmalicine  (ISO)
all-trans-retinoic acid  (ISO)
almotriptan  (ISO)
alpha-methyltryptamine  (ISO)
amiodarone  (EXP,ISO)
amitriptyline  (ISO)
amitriptylinoxide  (ISO)
ammonium chloride  (EXP)
amodiaquine  (ISO)
amphetamine  (ISO)
amphetamines  (ISO)
aniline  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atomoxetine hydrochloride  (ISO)
Auriculasin  (ISO)
bacitracin  (EXP)
barnidipine  (ISO)
benidipine  (ISO)
benzbromarone  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-carboline  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bortezomib  (ISO)
Bufuralol  (EXP,ISO)
buprenorphine  (ISO)
buspirone  (EXP,ISO)
butyric acid  (ISO)
C.I. Natural Red 20  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calciol  (ISO)
cannabidiol  (ISO)
Cannabidivarin  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbendazim  (ISO)
carbon nanotube  (ISO)
carvedilol  (ISO)
chelidonine  (ISO)
chlordecone  (ISO)
chloroquine  (ISO)
chlorphenamine  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cimetidine  (EXP,ISO)
cinacalcet  (ISO)
cisplatin  (EXP)
citalopram  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
clonidine  (ISO)
clonidine (amino form)  (ISO)
clonidine (imino form)  (ISO)
clopidogrel  (ISO)
clozapine  (ISO)
Clozapine N-oxide  (ISO)
codeine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corticosterone  (EXP)
coumarins  (ISO)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyhalothrin  (EXP,ISO)
cypermethrin  (ISO)
daidzein  (ISO)
dapsone  (ISO)
debrisoquin  (ISO)
Desethylchloroquine  (ISO)
desipramine  (ISO)
desloratadine  (ISO)
dexamethasone  (EXP,ISO)
dextromethorphan  (EXP,ISO)
dextrorphan  (ISO)
diarsenic trioxide  (ISO)
diarylheptanoid  (ISO)
diazinon  (ISO)
dibenz[a,h]anthracene  (ISO)
diclofenac  (ISO)
dihydrocapsaicin  (ISO)
Dihydrocorynantheine  (ISO)
dihydroergotamine  (ISO)
dimemorfan  (ISO)
dimethocaine  (ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
domperidone  (ISO)
dopamine  (ISO)
dronedarone  (ISO)
ellipticine  (ISO)
endosulfan  (EXP)
erythromycin A  (ISO)
ethambutol  (ISO)
ethanol  (ISO)
eugenol  (ISO)
eupatorin  (ISO)
fenofibrate  (EXP)
fenproporex  (ISO)
fenvalerate  (ISO)
fipronil  (ISO)
fipronil-sulfone  (ISO)
flavonoids  (EXP)
fluoxetine  (ISO)
flutamide  (EXP,ISO)
folic acid  (ISO)
formononetin  (ISO)
furan  (EXP)
gallocatechin  (ISO)
gamma-hexachlorocyclohexane  (ISO)
gefitinib  (ISO)
glafenine  (EXP)
glutathione  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
haloperidol  (ISO)
hemin  (ISO)
HET0016  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hydroxychloroquine  (ISO)
hyodeoxycholic acid  (EXP)
Hypaconitine  (ISO)
ifosfamide  (ISO)
imipramine  (ISO)
imipramine oxide  (ISO)
imiquimod  (ISO)
isatin  (ISO)
isocarbophos  (ISO)
isoimperatorin  (ISO)
isoproturon  (ISO)
ivermectin  (ISO)
ketoconazole  (ISO)
kojic acid  (EXP)
L-ethionine  (EXP)
L-methionine  (ISO)
lamotrigine  (ISO)
lefetamine  (ISO)
Licochalcone A  (ISO)
lipoic acid  (ISO)
lithocholic acid  (EXP,ISO)
Loratadine  (ISO)
loxapine  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
mangiferin  (ISO)
manidipine  (ISO)
Melarsoprol  (ISO)
Mequitazine  (ISO)
methadone  (ISO)
methamphetamine  (ISO)
methapyrilene  (EXP)
methiocarb  (ISO)
methiocarb-sulfoxide  (ISO)
methoxsalen  (ISO)
methoxychlor  (ISO)
metoclopramide  (ISO)
metoprolol  (ISO)
midazolam  (ISO)
Mitragynine  (ISO)
monosodium L-glutamate  (ISO)
morphine  (ISO)
myricetin  (ISO)
N,N-Didesmethyltamoxifen  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N,N-diisopropyltryptamine  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-desmethylclozapine  (ISO)
N-Desmethyltamoxifen  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
naphthalene  (ISO)
Neferine  (ISO)
nicardipine  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nifedipine  (ISO)
nimesulide  (ISO)
Norbuprenorphine  (ISO)
norcodeine  (ISO)
nortriptyline  (ISO)
Notopterol  (ISO)
o-anisidine  (ISO)
O-methyleugenol  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (EXP)
olivetol  (ISO)
omeprazole  (EXP,ISO)
Ondansetron  (ISO)
Oxatomide  (ISO)
oxycodone  (ISO)
ozagrel  (EXP)
p-cresol  (ISO)
paclitaxel  (ISO)
paliperidone palmitate  (ISO)
paraquat  (ISO)
parathion  (ISO)
paroxetine  (ISO)
pentamidine  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
perhexiline  (ISO)
phenanthrene  (ISO)
phencyclidine  (ISO)
phenobarbital  (EXP,ISO)
phenthoate  (ISO)
phenytoin  (ISO)
PhIP  (ISO)
phlorizin  (ISO)
pirinixic acid  (EXP,ISO)
poly(styrene)  (ISO)
potassium bromate  (ISO)
potassium dichromate  (ISO)
primaquine  (ISO)
prochloraz  (ISO)
proguanil  (ISO)
promethazine  (ISO)
propafenone  (ISO)
propranolol  (ISO)
pyrantel  (ISO)
pyrazinecarboxamide  (EXP)
pyrrolidines  (ISO)
quercetin  (ISO)
quinidine  (EXP,ISO)
quinine  (EXP)
resveratrol  (ISO)
rifampicin  (ISO)
risperidone  (ISO)
ritonavir  (ISO)
rotenone  (EXP)
Sabeluzole  (ISO)
safrole  (ISO)
Salinomycin  (ISO)
saracatinib  (ISO)
sarpogrelate  (ISO)
Senkirkine  (ISO)
serpentine  (ISO)
sertraline  (ISO)
Shikonin  (ISO)
sibutramine  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sophoranone  (ISO)
sparteine  (ISO)
Sudan I  (ISO)
sulindac  (EXP)
tamoxifen  (ISO)
tegaserod  (ISO)
terbinafine  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thioridazine  (ISO)
ticlopidine  (ISO)
titanium dioxide  (ISO)
tofacitinib  (ISO)
tolterodine tartrate  (ISO)
toluene  (EXP)
tramadol  (ISO)
trans-cinnamic acid  (ISO)
tranylcypromine  (ISO)
triclosan  (ISO)
triflumuron  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tryptamines  (ISO)
tyramine  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
veliparib  (ISO)
venlafaxine hydrochloride  (ISO)
verapamil  (ISO)
vinclozolin  (EXP)
warfarin  (ISO)
yohimbine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Bromek E, etal., Eur J Pharmacol. 2010 Jan 25;626(2-3):171-8. Epub 2009 Oct 8.
2. Dickmann LJ, etal., Biochem Pharmacol. 2008 Apr 15;75(8):1677-87. Epub 2008 Feb 7.
3. Fedorova IuIu, etal., Mol Biol (Mosk). 2009 Nov-Dec;43(6):1032-9.
4. Gaedigk A, etal., Am J Hum Genet 1991 May;48(5):943-50.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Gilbert EA, etal., J Neural Transm 2003 Oct;110(10):1091-101.
7. GOA data from the GO Consortium
8. Haduch A, etal., Pharmacol Res. 2013 Jan;67(1):53-9. doi: 10.1016/j.phrs.2012.10.009. Epub 2012 Oct 23.
9. Ishida N, etal., Biochem Biophys Res Commun 1988 Oct 31;156(2):681-8.
10. Kawashima H and Strobel HW, Biochem Biophys Res Commun 1995 Apr 17;209(2):535-40.
11. Kawashima H, etal., J Biol Chem 1996 Nov 8;271(45):28176-80.
12. Kishimoto W, etal., Endocrinology. 2004 Feb;145(2):699-705. Epub 2003 Oct 16.
13. MGD data from the GO Consortium
14. Miyakawa H, etal., Autoimmunity. 1999;30(2):107-14.
15. Mizuno D, etal., Biochim Biophys Acta 2003 Jun 19;1627(2-3):121-8.
16. Mizuno D, etal., Osaka City Med J. 2003 Jun;49(1):49-56.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nikoloff D, etal., Pharmacogenomics J 2002;2(6):400-7.
19. OMIM Disease Annotation Pipeline
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Pipeline to import SMPDB annotations from SMPDB into RGD
22. Polonikov AV, etal., J Hum Genet. 2009 Aug;54(8):440-9. Epub 2009 Jul 3.
23. Remmers EF, etal., Transplant Proc 1999 May;31(3):1549-54.
24. RGD automated data pipeline
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. RGD comprehensive gene curation
28. Roddam PL, etal., Pharmacogenetics. 2000 Oct;10(7):605-15.
29. Silveira Vda S, etal., Environ Mol Mutagen. 2010 Jan;51(1):48-56. doi: 10.1002/em.20510.
30. Thompson CM, etal., J Pharmacol Exp Ther. 2000 Sep;294(3):1120-30.
31. Vangsted AJ, etal., BMC Cancer. 2010 Aug 4;10:404. doi: 10.1186/1471-2407-10-404.
32. Wang N, etal., Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2011 Apr;19(2):327-31.
33. Zhang J, etal., Int J Environ Res Public Health. 2016 Aug 1;13(8). pii: ijerph13080776. doi: 10.3390/ijerph13080776.
34. Zhu Z, etal., Biochem Biophys Res Commun 2002 Sep 13;297(1):65.
Additional References at PubMed
PMID:2107330   PMID:7712118   PMID:9434752   PMID:10681376   PMID:11032406   PMID:12477932   PMID:12865317   PMID:15039299   PMID:15327587   PMID:16352597   PMID:16401082   PMID:18356043  
PMID:19219744   PMID:19420131   PMID:19438707   PMID:19448135   PMID:19651758   PMID:21289075   PMID:22162298   PMID:23235327   PMID:23623752  


Genomics

Comparative Map Data
Cyp2d4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,882,584 - 113,891,754 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,881,618 - 113,891,759 (-)Ensembl
Rnor_6.07123,599,264 - 123,608,436 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,599,266 - 123,608,436 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,583,983 - 123,593,008 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,742,273 - 120,752,274 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,775,536 - 120,786,502 (-)NCBI
Celera7110,197,422 - 110,206,650 (-)NCBICelera
Cytogenetic Map7q34NCBI
CYP2D6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2242,126,499 - 42,130,865 (-)EnsemblGRCh38hg38GRCh38
GRCh382242,126,499 - 42,130,810 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372242,522,501 - 42,526,812 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,852,445 - 40,856,827 (-)NCBINCBI36hg18NCBI36
Build 342240,847,000 - 40,851,379NCBI
Celera2226,328,694 - 26,333,076 (-)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2225,488,519 - 25,492,901 (-)NCBIHuRef
CHM1_12242,482,242 - 42,486,624 (-)NCBICHM1_1
Cyp2d22
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391582,254,728 - 82,264,461 (-)NCBIGRCm39mm39
GRCm39 Ensembl1582,254,728 - 82,264,461 (-)Ensembl
GRCm381582,370,527 - 82,380,260 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1582,370,527 - 82,380,260 (-)EnsemblGRCm38mm10GRCm38
MGSCv371582,200,957 - 82,210,690 (-)NCBIGRCm37mm9NCBIm37
MGSCv361582,199,236 - 82,207,926 (-)NCBImm8
Celera1584,494,227 - 84,513,082 (-)NCBICelera
Cytogenetic Map15E1NCBI
CYP2D15
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,255,259 - 23,259,380 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1023,255,249 - 23,259,298 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,190,268 - 23,194,223 (+)NCBI
ROS_Cfam_1.01024,000,262 - 24,004,211 (+)NCBI
UMICH_Zoey_3.11023,717,484 - 23,721,432 (+)NCBI
UNSW_CanFamBas_1.01024,037,966 - 24,041,898 (+)NCBI
UU_Cfam_GSD_1.01024,212,712 - 24,216,661 (+)NCBI
LOC101961588
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049456,804,025 - 6,843,868 (+)NCBI
SpeTri2.0NW_004936718153,340 - 157,966 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYP2D6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,538,907 - 6,543,643 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.156,539,021 - 6,543,643 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.253,810,426 - 3,815,068 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CYP2D6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,667,207 - 24,672,580 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1924,667,282 - 24,671,513 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045100,727,530 - 100,732,209 (+)NCBIVero_WHO_p1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:122
Count of miRNA genes:107
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000011880
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 2 12 12 12 15 5 1 8
Low 1 43 45 29 19 29 8 11 59 30 36 3 8
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011880   ⟹   ENSRNOP00000011880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,881,618 - 113,891,759 (-)Ensembl
Rnor_6.0 Ensembl7123,599,266 - 123,608,436 (-)Ensembl
RefSeq Acc Id: NM_138515   ⟹   NP_612524
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,882,584 - 113,891,743 (-)NCBI
Rnor_6.07123,599,264 - 123,608,436 (-)NCBI
Rnor_5.07123,583,983 - 123,593,008 (-)NCBI
RGSC_v3.47120,742,273 - 120,752,274 (-)RGD
Celera7110,197,422 - 110,206,650 (-)RGD
Sequence:
RefSeq Acc Id: XM_039078359   ⟹   XP_038934287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,883,929 - 113,891,754 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_612524   ⟸   NM_138515
- UniProtKB: Q64680 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011880   ⟸   ENSRNOT00000011880
RefSeq Acc Id: XP_038934287   ⟸   XM_039078359
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13695535
Promoter ID:EPDNEW_R6060
Type:multiple initiation site
Name:Cyp2d4_1
Description:cytochrome P450, family 2, subfamily d, polypeptide 4
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_6.07123,608,452 - 123,608,512EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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)
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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
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)
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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/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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 123584058 123584059 G T snv BBDP/WorN (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 123599339 123599340 G T snv BBDP/Wor (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620640 AgrOrtholog
Ensembl Genes ENSRNOG00000032261 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011880 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011880 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.630.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7319137 IMAGE-MGC_LOAD
InterPro Cyt_P450 UniProtKB/Swiss-Prot
  Cyt_P450_CS UniProtKB/Swiss-Prot
  Cyt_P450_E_grp-I UniProtKB/Swiss-Prot
  Cyt_P450_E_grp-I_CYP2D-like UniProtKB/Swiss-Prot
  Cyt_P450_sf UniProtKB/Swiss-Prot
KEGG Report rno:171522 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105324 IMAGE-MGC_LOAD
NCBI Gene 171522 ENTREZGENE
Pfam p450 UniProtKB/Swiss-Prot
PharmGKB CYP2D6 RGD
PhenoGen Cyp2d4 PhenoGen
PRINTS EP450I UniProtKB/Swiss-Prot
  EP450ICYP2D UniProtKB/Swiss-Prot
  P450 UniProtKB/Swiss-Prot
PROSITE CYTOCHROME_P450 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48264 UniProtKB/Swiss-Prot
UniProt CP2D4_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35107 UniProtKB/Swiss-Prot
  P13108 UniProtKB/Swiss-Prot
  Q566D3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-19 Cyp2d4  cytochrome P450, family 2, subfamily D, polypeptide 4  Cyp2d4  cytochrome P450, family 2, subfamily D, polypeptide 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-19 Cyp2d4  cytochrome P450, family 2, subfamily d, polypeptide 4  Cyp2d4  cytochrome P450, family 2, subfamily D, polypeptide 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-19 Cyp2d4  cytochrome P450, family 2, subfamily D, polypeptide 4  Cyp2d4v1  cytochrome P450, family 2, subfamily d, polypeptide 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-07-06 Cyp2d4v1  cytochrome P450, family 2, subfamily d, polypeptide 4  Cyp2d22  cytochrome P450, family 2, subfamily d, polypeptide 22  Name updated 1299863 APPROVED
2007-04-23 Cyp2d22  cytochrome P450, family 2, subfamily d, polypeptide 22  Cyp2d6_mapped  cytochrome P450, subfamily IID, polypeptide 6 (mapped)  Data Merged 737654 APPROVED
2005-11-17 Cyp2d6_mapped  cytochrome P450, subfamily IID, polypeptide 6 (mapped)      Symbol and Name updated 1556543 APPROVED
2004-09-10 Cyp2d22  cytochrome P450, family 2, subfamily d, polypeptide 22  Cyp2d18  cytochrome P450 2d18  Symbol and Name updated 1299863 APPROVED
2003-04-09 Cyp2d18  cytochrome P450 2d18      Symbol and Name updated 629477 APPROVED
2003-04-09 Cyp2d6  cytochrome P450, subfamily IID, polypeptide 6    cytochrome P450, subfamily 2D, polypeptide 6  Symbol and Name status set to approved 629479 APPROVED
2003-03-07 Cyp2d18  cytochrome P450 2d18  Cyp2d4  Cytochrome P450, subfamily IID4  Data Merged 628472 PROVISIONAL
2002-08-07 Cyp2d18  cytochrome P450 2D18      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Cyp2d4  Cytochrome P450, subfamily IID4      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Cyp2d6  cytochrome P450, subfamily 2D, polypeptide 6      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in skin but not in liver 625597