Mthfr (methylenetetrahydrofolate reductase) - Rat Genome Database

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Gene: Mthfr (methylenetetrahydrofolate reductase) Rattus norvegicus
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Symbol: Mthfr
Name: methylenetetrahydrofolate reductase
RGD ID: 1309952
Description: Enables NADP binding activity; flavin adenine dinucleotide binding activity; and methylenetetrahydrofolate reductase (NAD(P)H) activity. Involved in several processes, including homocysteine metabolic process; response to interleukin-1; and response to vitamin. Located in cytosol and synapse. Biomarker of hyperthyroidism; hypothyroidism; and liver benign neoplasm. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); cardiovascular system disease (multiple); hematologic cancer (multiple); and kidney failure (multiple). Orthologous to human MTHFR (methylenetetrahydrofolate reductase); PARTICIPATES IN altered folate cycle metabolic pathway; altered folate mediated one-carbon metabolic pathway; folate cycle metabolic pathway; INTERACTS WITH 2-acetamidofluorene; 3-chloropropane-1,2-diol; aflatoxin B1.
Type: protein-coding
RefSeq Status: MODEL
Also known as: 5,10-methylenetetrahydrofolate reductase; 5,10-methylenetetrahydrofolate reductase (NADPH); LOC362657; methylenetetrahydrofolate reductase (NAD(P)H)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Mthfrem1Mcwi  
Genetic Models: SS-Mthfrem1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25158,465,248 - 158,484,999 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5158,465,296 - 158,483,797 (+)Ensembl
Rnor_6.05164,844,642 - 164,864,360 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5164,845,925 - 164,860,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05168,502,556 - 168,522,350 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,112,850 - 165,126,885 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15165,123,406 - 165,137,073 (+)NCBI
Celera5156,747,024 - 156,766,742 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (ISO)
acute kidney failure  (ISO)
acute lymphoblastic leukemia  (ISO)
acute myeloid leukemia  (ISO)
Albuminuria  (ISO)
alcoholic liver cirrhosis  (ISO)
allergic disease  (ISO)
alopecia  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
anemia  (ISO)
angle-closure glaucoma  (ISO)
ankylosing spondylitis  (ISO)
Aortic Coarctation  (ISO)
aphthous stomatitis  (ISO)
Arsenic Poisoning  (ISO)
Arterial Occlusive Diseases  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
attention deficit hyperactivity disorder  (ISO)
autistic disorder  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
Banti's Syndrome  (ISO)
bipolar disorder  (ISO)
brain ischemia  (ISO)
Breast Neoplasms  (ISO)
Budd-Chiari syndrome  (ISO)
cardia cancer  (ISO)
cardiovascular system disease  (ISO)
carotid stenosis  (ISO)
cataract  (ISO)
cerebral infarction  (ISO)
cervical cancer  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
cholangiocarcinoma  (ISO)
chronic kidney disease  (ISO)
chronic myeloid leukemia  (ISO)
clear cell renal cell carcinoma  (ISO)
cleft lip  (ISO)
clubfoot  (ISO)
Colonic Neoplasms  (ISO)
Colorectal Neoplasms  (ISO)
congenital heart disease  (ISO)
Conotruncal Cardiac Defects  (ISO)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
coronary restenosis  (ISO)
Crohn's disease  (ISO)
Cytomegalovirus Infections  (ISO)
Developmental Disabilities  (ISO)
dextro-looped transposition of the great arteries  (ISO)
diabetes mellitus  (ISO)
diabetic angiopathy  (ISO)
Diabetic Nephropathies  (ISO)
diabetic retinopathy  (ISO)
diffuse large B-cell lymphoma  (ISO)
Down syndrome  (ISO)
Drug Eruptions  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
end stage renal disease  (ISO)
Endometrial Neoplasms  (ISO)
Experimental Diabetes Mellitus  (IEP)
eye disease  (ISO)
factor VIII deficiency  (ISO)
Familial Atrial Fibrillation 6  (ISO)
familial Mediterranean fever  (ISO)
fatty liver disease  (ISO)
Female Infertility  (ISO)
Folate-Sensitive Neural Tube Defects  (ISO)
follicular lymphoma  (ISO)
Gastrointestinal Diseases  (ISO)
gastrointestinal stromal tumor  (ISO)
glomerulonephritis  (ISO)
Graft vs Host Disease  (ISO)
Graves' disease  (ISO)
Habitual Abortions  (ISO)
Hearing Loss  (ISO)
Helicobacter Infections  (ISO)
Hematologic Neoplasms  (ISO)
hematopoietic system disease  (ISO)
hepatic veno-occlusive disease  (ISO)
hepatitis B  (ISO)
hepatocellular carcinoma  (ISO)
homocystinuria  (ISS)
hyperhomocysteinemia  (ISO)
hyperthyroidism  (IEP)
hypopituitarism  (ISO)
hypothyroidism  (IEP)
inflammatory bowel disease  (ISO)
Inherited Blood Coagulation Disease  (ISO)
intellectual disability  (ISO)
intracranial sinus thrombosis  (ISO)
ischemia  (ISO)
kidney disease  (ISO)
kidney failure  (ISO)
Kuhnt-Junius degeneration  (ISO)
Left Ventricular Hypertrophy  (ISO)
Leukoencephalopathies  (ISO)
leukopenia  (ISO)
liver benign neoplasm  (IEP)
liver cirrhosis  (ISO)
liver disease  (ISO)
Lung Neoplasms  (ISO)
lung small cell carcinoma  (ISO)
lymphoma  (ISO)
male infertility  (ISO)
Malnutrition  (ISO)
Maxillofacial Abnormalities  (ISO)
Meniere's disease  (ISO)
mental depression  (ISO)
Methylenetetrahydrofolate Reductase Deficiency  (ISO)
Microsatellite Instability  (ISO)
Microvascular Angina  (ISO)
migraine  (ISO)
migraine with aura  (ISO)
mitral valve disease  (ISO)
Mthfr Deficiency, Thermolabile Type  (ISO)
mucositis  (ISO)
multiple myeloma  (ISO)
myeloid neoplasm  (ISO)
myelomeningocele  (ISO)
myocardial infarction  (ISO)
Necrosis  (ISO)
Neoplasm Metastasis  (ISO)
nephroblastoma  (ISO)
nephrosclerosis  (ISO)
nervous system disease  (ISO)
neural tube defect  (ISO)
neutropenia  (ISO)
non-alcoholic fatty liver disease  (ISO)
non-arteritic anterior ischemic optic neuropathy  (ISO)
non-Hodgkin lymphoma  (ISO)
open-angle glaucoma  (ISO)
oral squamous cell carcinoma  (ISO)
osteonecrosis  (ISO)
osteosarcoma  (ISO)
pancreatic cancer  (ISO)
papillomavirus infectious disease  (ISO)
Parkinson's disease  (ISO)
peripheral artery disease  (ISO)
portal vein thrombosis  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
pulmonary embolism  (ISO)
rectal benign neoplasm  (ISO)
renal artery disease  (ISO)
renal cell carcinoma  (ISO)
retinal disease  (ISO)
retinal vein occlusion  (ISO)
rheumatoid arthritis  (ISO)
schizophrenia  (ISO)
sickle cell anemia  (ISO)
skin disease  (ISO)
smallpox  (ISO)
spina bifida  (ISO)
spinal cord disease  (ISO)
sporadic breast cancer  (ISO)
squamous cell carcinoma  (ISO)
stomach cancer  (ISO)
Stomach Neoplasms  (ISO)
Stroke  (ISO)
Sudden Hearing Loss  (ISO)
tetralogy of Fallot  (ISO)
thrombocytopenia  (ISO)
thrombophilia  (ISO)
thrombophilia due to thrombin defect  (ISO)
thrombosis  (ISO)
Thrombotic Microangiopathies  (ISO)
thyrotoxicosis  (ISO)
transitional cell carcinoma  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
urinary bladder cancer  (ISO)
Uterine Cervical Neoplasms  (ISO)
Vascular Calcification  (ISO)
vascular disease  (ISO)
Venous Thromboembolism  (ISO)
Venous Thrombosis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
3-chloropropane-1,2-diol  (EXP)
5,10-methylenetetrahydrofolic acid  (ISO)
5-fluorouracil  (ISO)
5-formyltetrahydrofolic acid  (ISO)
5-methyltetrahydrofolic acid  (ISO)
7-Hydroxymethotrexate  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
ancitabine  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benazepril  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bifenthrin  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
clozapine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyanocob(III)alamin  (EXP)
cyproconazole  (EXP)
cytarabine  (ISO)
dibenz[a,h]anthracene  (ISO)
epoxiconazole  (EXP)
floxuridine  (ISO)
folic acid  (EXP,ISO)
gallic acid  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
GW 4064  (ISO)
homocysteine  (ISO)
indole-3-methanol  (EXP)
L-methionine  (ISO)
maneb  (ISO)
methotrexate  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nickel atom  (ISO)
olanzapine  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
pentanal  (ISO)
phenylhydrazine  (EXP)
pirinixic acid  (ISO)
raloxifene  (ISO)
riboflavin  (ISO)
ritodrine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulfasalazine  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetrahydrocurcumin  (ISO)
tributylstannane  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vigabatrin  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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Additional References at PubMed
PMID:10551815   PMID:12673793   PMID:15217352   PMID:20031578   PMID:24769206   PMID:25736335   PMID:25855017   PMID:29222906  


Genomics

Comparative Map Data
Mthfr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25158,465,248 - 158,484,999 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5158,465,296 - 158,483,797 (+)Ensembl
Rnor_6.05164,844,642 - 164,864,360 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5164,845,925 - 164,860,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05168,502,556 - 168,522,350 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,112,850 - 165,126,885 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15165,123,406 - 165,137,073 (+)NCBI
Celera5156,747,024 - 156,766,742 (+)NCBICelera
Cytogenetic Map5q36NCBI
MTHFR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl111,785,723 - 11,806,455 (-)EnsemblGRCh38hg38GRCh38
GRCh38111,785,723 - 11,806,103 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37111,845,780 - 11,866,021 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36111,768,374 - 11,788,702 (-)NCBINCBI36hg18NCBI36
Build 34111,780,944 - 11,800,248NCBI
Celera110,959,433 - 10,979,782 (-)NCBI
Cytogenetic Map1p36.22NCBI
HuRef111,000,872 - 11,021,217 (-)NCBIHuRef
CHM1_1111,833,709 - 11,854,054 (-)NCBICHM1_1
Mthfr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394148,123,534 - 148,144,019 (+)NCBIGRCm39mm39
GRCm39 Ensembl4148,123,534 - 148,144,008 (+)Ensembl
GRCm384148,039,077 - 148,059,562 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4148,039,077 - 148,059,551 (+)EnsemblGRCm38mm10GRCm38
MGSCv374147,413,186 - 147,433,671 (+)NCBIGRCm37mm9NCBIm37
MGSCv364146,885,022 - 146,903,349 (+)NCBImm8
Celera4150,305,674 - 150,326,065 (+)NCBICelera
Cytogenetic Map4E1NCBI
cM Map478.67NCBI
Mthfr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554862,096,379 - 2,112,240 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554862,096,379 - 2,112,240 (+)NCBIChiLan1.0ChiLan1.0
MTHFR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1111,766,334 - 11,785,645 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl111,766,334 - 11,785,419 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0110,548,196 - 10,568,174 (-)NCBIMhudiblu_PPA_v0panPan3
MTHFR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1284,445,526 - 84,457,435 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl284,380,919 - 84,536,818 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha280,977,302 - 80,990,296 (+)NCBI
ROS_Cfam_1.0285,109,058 - 85,123,378 (+)NCBI
UMICH_Zoey_3.1281,858,180 - 81,870,539 (+)NCBI
UNSW_CanFamBas_1.0282,857,476 - 82,872,293 (+)NCBI
UU_Cfam_GSD_1.0283,920,334 - 83,933,329 (+)NCBI
Mthfr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505834,798,656 - 34,813,131 (-)NCBI
SpeTri2.0NW_004936474623,438 - 637,849 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MTHFR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl671,863,636 - 71,881,820 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1671,863,637 - 71,882,118 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2665,776,804 - 65,791,405 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MTHFR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120119,987,667 - 120,003,611 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20119,990,133 - 120,002,950 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605423,855,633 - 23,871,475 (+)NCBIVero_WHO_p1.0
Mthfr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248181,184,736 - 1,202,708 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat


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

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:91
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000011384
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 4 2 2 2 51 35 32
Low 3 39 55 39 19 39 8 11 23 9 11 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001074061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_342975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC094126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U57049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011384   ⟹   ENSRNOP00000011384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5158,465,296 - 158,483,797 (+)Ensembl
Rnor_6.0 Ensembl5164,845,925 - 164,860,910 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102508   ⟹   ENSRNOP00000085916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5158,467,151 - 158,483,797 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118752   ⟹   ENSRNOP00000086290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5158,465,415 - 158,483,797 (+)Ensembl
RefSeq Acc Id: XM_006239413   ⟹   XP_006239475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25158,465,774 - 158,484,999 (+)NCBI
Rnor_6.05164,845,192 - 164,864,360 (+)NCBI
Rnor_5.05168,502,556 - 168,522,350 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239414   ⟹   XP_006239476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25158,465,248 - 158,484,999 (+)NCBI
Rnor_6.05164,844,642 - 164,864,360 (+)NCBI
Rnor_5.05168,502,556 - 168,522,350 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239416   ⟹   XP_006239478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25158,465,392 - 158,484,999 (+)NCBI
Rnor_6.05164,844,754 - 164,864,360 (+)NCBI
Rnor_5.05168,502,556 - 168,522,350 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239417   ⟹   XP_006239479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25158,465,392 - 158,484,999 (+)NCBI
Rnor_6.05164,844,754 - 164,864,360 (+)NCBI
Rnor_5.05168,502,556 - 168,522,350 (+)NCBI
Sequence:
RefSeq Acc Id: XM_342975   ⟹   XP_342976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25158,465,777 - 158,484,999 (+)NCBI
Rnor_6.05164,845,192 - 164,864,360 (+)NCBI
Rnor_5.05168,502,556 - 168,522,350 (+)NCBI
RGSC_v3.45165,112,850 - 165,126,885 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_342976   ⟸   XM_342975
- Peptide Label: isoform X1
- UniProtKB: D4A7E8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239476   ⟸   XM_006239414
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006239478   ⟸   XM_006239416
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006239479   ⟸   XM_006239417
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006239475   ⟸   XM_006239413
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000011384   ⟸   ENSRNOT00000011384
RefSeq Acc Id: ENSRNOP00000086290   ⟸   ENSRNOT00000118752
RefSeq Acc Id: ENSRNOP00000085916   ⟸   ENSRNOT00000102508

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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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
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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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
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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)
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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
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)
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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
M520/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
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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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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)
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)
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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)
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 168514771 168514772 C G snv WKY/N (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/NHsd (KNAW), WKY/NCrl (KNAW), DOB/Oda (KyushuU)
5 168518638 168518639 T G snv SR/JrHsd (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 158477420 158477421 C G snv SHRSP/A3NCrl (2019), WKY/N (2020), WKY/NCrl (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 164856781 164856782 C G snv SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/N (2020), SHRSP/A3NCrl (2019), WKY/NCrl (2019), WKY/NHsd (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 165122954 165122955 C G snv SHRSP/Gcrc (MDC), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL)
5 165126821 165126822 T G snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309952 AgrOrtholog
Ensembl Genes ENSRNOG00000008553 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011384 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011384 UniProtKB/TrEMBL
InterPro FAD-linked_oxidoreductase-like UniProtKB/TrEMBL
  Fadh2_euk UniProtKB/TrEMBL
  Mehydrof_redctse UniProtKB/TrEMBL
NCBI Gene 362657 ENTREZGENE
Pfam MTHFR UniProtKB/TrEMBL
PharmGKB MTHFR RGD
PhenoGen Mthfr PhenoGen
Superfamily-SCOP SSF51730 UniProtKB/TrEMBL
TIGRFAMs fadh2_euk UniProtKB/TrEMBL
UniProt D4A7E8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-12-16 Mthfr  methylenetetrahydrofolate reductase (NAD(P)H)  Mthfr  5,10-methylenetetrahydrofolate reductase (NADPH)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Mthfr  5,10-methylenetetrahydrofolate reductase (NADPH)  Mthfr  5,10-methylenetetrahydrofolate reductase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-17 Mthfr  5,10-methylenetetrahydrofolate reductase  Mthfr_predicted  5,10-methylenetetrahydrofolate reductase (NADPH) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Mthfr_predicted  5,10-methylenetetrahydrofolate reductase (NADPH) (predicted)      Symbol and Name status set to approved 70820 APPROVED