Dhfr (dihydrofolate reductase) - Rat Genome Database

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Gene: Dhfr (dihydrofolate reductase) Rattus norvegicus
Analyze
Symbol: Dhfr
Name: dihydrofolate reductase
RGD ID: 2500
Description: Exhibits NADP binding activity; dihydrofolate reductase activity; and dihydrofolic acid binding activity. Involved in several processes, including axon regeneration; folic acid-containing compound metabolic process; and response to methotrexate. Localizes to mitochondrion. Human ortholog(s) of this gene implicated in acute lymphoblastic leukemia. Orthologous to several human genes including DHFR2 (dihydrofolate reductase 2) and DHFRP1 (dihydrofolate reductase pseudogene 1); PARTICIPATES IN folate mediated one-carbon metabolic pathway; folate metabolic pathway; pyrimidine metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Dhfr1; Dihydrofolate reductase 1 (active)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2223,585,876 - 23,611,199 (+)NCBI
Rnor_6.0 Ensembl221,931,493 - 21,962,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0221,931,887 - 21,958,927 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0241,137,784 - 41,149,417 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0241,162,308 - 41,162,496 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4222,607,093 - 22,828,487 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1222,527,461 - 22,748,856 (+)NCBI
Celera219,675,965 - 19,700,103 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(+)-schisandrin B  (EXP)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
5-formyltetrahydrofolic acid  (ISO)
6-bromoindirubin-3'-oxime  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-carotene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
captan  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefazolin  (ISO)
cefepime  (ISO)
ceftazidime pentahydrate  (ISO)
ceftizoxime  (ISO)
ceftriaxone  (ISO)
chlorambucil  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
DISTAMYCIN A  (ISO)
doxorubicin  (ISO)
emodin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (ISO)
ferulic acid  (ISO)
folic acid  (EXP,ISO)
folpet  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
gentamycin  (EXP)
indometacin  (EXP)
isoflavones  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
leflunomide  (EXP)
levofloxacin  (ISO)
Mecamylamine  (ISO)
methapyrilene  (ISO)
methotrexate  (EXP,ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
naringin  (ISO)
nickel atom  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
nitrogen mustard  (ISO)
olmesartan  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
pemetrexed  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
Rebamipide  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sunitinib  (ISO)
syringic acid  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
topotecan  (EXP)
trabectedin  (ISO)
trimellitic anhydride  (ISO)
trimethoprim  (ISO)
trimetrexate  (ISO)
triptonide  (ISO)
tubocurarine  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)

References

References - curated
1. Al-Shakfa F, etal., Clin Cancer Res. 2009 Nov 15;15(22):6931-8. doi: 10.1158/1078-0432.CCR-09-0641. Epub 2009 Oct 27.
2. Cario H, etal., Am J Hum Genet. 2011 Feb 11;88(2):226-31. doi: 10.1016/j.ajhg.2011.01.007.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Gewirtz DA, etal., Cancer Res. 1980 Mar;40(3):573-8.
5. GOA data from the GO Consortium
6. Gomez-Gomez Y, etal., Exp Ther Med. 2012 Apr;3(4):665-672. Epub 2012 Jan 9.
7. Guo J, etal., J Biol Chem. 2005 Aug 26;280(34):30422-31. Epub 2005 Jun 27.
8. Hughes L, etal., FEBS Lett. 2015 Jul 8;589(15):1855-62. doi: 10.1016/j.febslet.2015.05.017. Epub 2015 May 14.
9. Iskandar BJ, etal., J Clin Invest. 2010 May;120(5):1603-16. doi: 10.1172/JCI40000. Epub 2010 Apr 26.
10. Levy AS, etal., J Pediatr Hematol Oncol. 2003 Sep;25(9):688-95.
11. Lucke-Huhle C Carcinogenesis. 1994 Apr;15(4):695-700.
12. Matherly LH, etal., Blood. 1997 Jul 15;90(2):578-89.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pipeline to import SMPDB annotations from SMPDB into RGD
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. RGD comprehensive gene curation
22. Seujange Y, etal., Am J Nephrol. 2008;28(4):692-700. doi: 10.1159/000126927. Epub 2008 Apr 11.
23. Stover PJ and Field MS, Adv Nutr. 2011 Jul;2(4):325-31. doi: 10.3945/┬┐an.111.000596. Epub 2011 Jun 28.
24. Sweeney CL, etal., Cancer Res. 2003 Mar 15;63(6):1304-10.
25. Wang Y, etal., Antimicrob Agents Chemother 2001 Sep;45(9):2517-23.
26. Watkins D and Rosenblatt DS, J Inherit Metab Dis. 2012 Jul;35(4):665-70. doi: 10.1007/s10545-011-9418-1. Epub 2011 Nov 23.
27. Webber S and Whiteley JM, Arch Biochem Biophys. 1985 Feb 1;236(2):681-90.
Additional References at PubMed
PMID:2303423   PMID:8490020   PMID:12096917   PMID:12477932   PMID:14667810   PMID:15039552   PMID:15974594   PMID:19666465   PMID:21876184   PMID:23707606  


Genomics

Comparative Map Data
Dhfr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2223,585,876 - 23,611,199 (+)NCBI
Rnor_6.0 Ensembl221,931,493 - 21,962,453 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0221,931,887 - 21,958,927 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0241,137,784 - 41,149,417 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0241,162,308 - 41,162,496 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4222,607,093 - 22,828,487 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1222,527,461 - 22,748,856 (+)NCBI
Celera219,675,965 - 19,700,103 (+)NCBICelera
Cytogenetic Map2q12NCBI
DHFR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl580,626,226 - 80,654,983 (-)EnsemblGRCh38hg38GRCh38
GRCh38580,626,226 - 80,654,983 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37579,922,045 - 79,950,802 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36579,957,801 - 79,986,556 (-)NCBINCBI36hg18NCBI36
Build 34579,957,803 - 79,986,572NCBI
Celera575,825,049 - 75,854,857 (-)NCBI
Cytogenetic Map5q14.1NCBI
HuRef575,130,997 - 75,159,721 (-)NCBIHuRef
CHM1_1579,355,281 - 79,384,046 (-)NCBICHM1_1
Dhfr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391392,491,291 - 92,525,561 (+)NCBIGRCm39mm39
GRCm39 Ensembl1392,491,234 - 92,525,561 (+)Ensembl
GRCm381392,354,783 - 92,389,053 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1392,354,726 - 92,389,053 (+)EnsemblGRCm38mm10GRCm38
MGSCv371393,124,738 - 93,159,008 (+)NCBIGRCm37mm9NCBIm37
MGSCv361393,455,536 - 93,489,806 (+)NCBImm8
Celera1395,961,012 - 95,994,907 (+)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1347.64NCBI
Dhfr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541829,274,170 - 29,283,028 (+)NCBIChiLan1.0ChiLan1.0
DHFR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1534,938,548 - 34,967,003 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl534,938,548 - 34,967,003 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0534,663,210 - 34,689,467 (+)NCBIMhudiblu_PPA_v0panPan3
Dhfr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213182,542,580 - 182,561,929 (+)NCBI
SpeTri2.0NW_00493646967,962 - 83,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DHFR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1289,230,660 - 89,255,830 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2291,077,865 - 91,102,076 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DHFR
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1474,787,292 - 74,811,196 (-)NCBI
ChlSab1.1 Ensembl474,787,629 - 74,810,960 (-)Ensembl
Dhfr
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247431,446,643 - 1,462,319 (-)NCBI

Position Markers
BE121398  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0221,934,990 - 21,935,138NCBIRnor6.0
Rnor_5.0241,140,887 - 41,141,035UniSTSRnor5.0
RGSC_v3.4222,610,196 - 22,610,344UniSTSRGSC3.4
Celera219,679,068 - 19,679,216UniSTS
Cytogenetic Map2q12UniSTS
RH128352  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0222,023,201 - 22,023,395NCBIRnor6.0
Rnor_5.0241,226,672 - 41,226,866UniSTSRnor5.0
RGSC_v3.4222,686,665 - 22,686,859UniSTSRGSC3.4
Celera219,764,314 - 19,764,508UniSTS
Cytogenetic Map2q12UniSTS
RH133371  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q12UniSTS
RH134136  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0221,959,240 - 21,959,431NCBIRnor6.0
Rnor_5.0241,162,809 - 41,163,000UniSTSRnor5.0
RGSC_v3.44415,160 - 415,342UniSTSRGSC3.4
RGSC_v3.4222,828,800 - 22,828,991UniSTSRGSC3.4
Celera219,700,416 - 19,700,607UniSTS
Cytogenetic Map2q12UniSTS
AW555094  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.043,086,611 - 3,086,693NCBIRnor6.0
Rnor_6.0221,959,350 - 21,959,432NCBIRnor6.0
Rnor_5.043,139,041 - 3,139,123UniSTSRnor5.0
Rnor_5.0241,162,919 - 41,163,001UniSTSRnor5.0
RGSC_v3.44415,262 - 415,344UniSTSRGSC3.4
RGSC_v3.4222,828,910 - 22,828,992UniSTSRGSC3.4
Celera219,700,526 - 19,700,608UniSTS
Celera45,137,637 - 5,137,719UniSTS
Cytogenetic Map2q12UniSTS
BI302236  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0222,154,173 - 22,154,322NCBIRnor6.0
Rnor_5.0241,357,420 - 41,357,569UniSTSRnor5.0
RGSC_v3.4222,818,070 - 22,818,219UniSTSRGSC3.4
Celera219,894,943 - 19,895,092UniSTS
Cytogenetic Map2q12UniSTS
RH141201  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0222,015,822 - 22,016,002NCBIRnor6.0
Rnor_5.0241,219,463 - 41,219,643UniSTSRnor5.0
RGSC_v3.4222,678,763 - 22,678,941UniSTSRGSC3.4
Celera219,757,016 - 19,757,196UniSTS
Cytogenetic Map2q12UniSTS
RH141424  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0222,106,277 - 22,106,481NCBIRnor6.0
Rnor_5.0241,309,463 - 41,309,667UniSTSRnor5.0
RGSC_v3.4222,769,741 - 22,769,945UniSTSRGSC3.4
Celera219,847,396 - 19,847,600UniSTS
Cytogenetic Map2q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135167060Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141179397Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)23127638105149020Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2368630848686308Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2541733642777046Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2789360052893600Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2944467949615930Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)2944467968866454Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21055527555555275Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21423783059237830Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21901646564016465Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22027698165276981Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22064137165641371Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:72
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000018259
Prediction methods: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 2 10 45 40 7 40 30 34 29
Low 1 33 12 1 12 1 8 9 44 1 11 11 8
Below cutoff 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018259   ⟹   ENSRNOP00000018259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl221,931,493 - 21,962,453 (+)Ensembl
RefSeq Acc Id: NM_130400   ⟹   NP_569084
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2223,585,996 - 23,610,192 (+)NCBI
Rnor_6.0221,931,887 - 21,958,927 (+)NCBI
Rnor_5.0241,137,784 - 41,149,417 (+)NCBI
Rnor_5.0241,162,308 - 41,162,496 (+)NCBI
RGSC_v3.4222,607,093 - 22,828,487 (+)RGD
Celera219,675,965 - 19,700,103 (+)RGD
Sequence:
RefSeq Acc Id: XM_039101710   ⟹   XP_038957638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2223,585,876 - 23,611,199 (+)NCBI
Protein Sequences
Protein RefSeqs NP_569084 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957638 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58584 (Get FASTA)   NCBI Sequence Viewer  
  AAL11500 (Get FASTA)   NCBI Sequence Viewer  
  EDM10015 (Get FASTA)   NCBI Sequence Viewer  
  Q920D2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_569084   ⟸   NM_130400
- UniProtKB: Q920D2 (UniProtKB/Swiss-Prot),   B0BMV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018259   ⟸   ENSRNOT00000018259
RefSeq Acc Id: XP_038957638   ⟸   XM_039101710
- Peptide Label: isoform X1
Protein Domains
DHFR

Transcriptome

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

Promoters
RGD ID:13691058
Promoter ID:EPDNEW_R1582
Type:initiation region
Name:Dhfr_1
Description:dihydrofolate reductase
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_6.0221,931,914 - 21,931,974EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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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 (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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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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 (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:2500 AgrOrtholog
Ensembl Genes ENSRNOG00000013521 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018259 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018259 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.430.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9022774 IMAGE-MGC_LOAD
InterPro DHFR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DHFR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DHFR_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DHFR_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:187341 IMAGE-MGC_LOAD
NCBI Gene 24312 ENTREZGENE
PANTHER PTHR48069 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DHFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB DHFR RGD
PhenoGen Dhfr PhenoGen
PROSITE DHFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DHFR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53597 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B0BMV8 ENTREZGENE, UniProtKB/TrEMBL
  DYR_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Dhfr  dihydrofolate reductase  Dhfr1  Dihydrofolate reductase 1 (active)  Symbol and Name updated 625702 APPROVED
2002-06-10 Dhfr1  Dihydrofolate reductase 1 (active)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process important for reducing dihydrofolate to tetrahydrofolate for subsequent purine and pyrimidine biosynthesis 1298877