Mdh1 (malate dehydrogenase 1) - Rat Genome Database

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Gene: Mdh1 (malate dehydrogenase 1) Rattus norvegicus
Analyze
Symbol: Mdh1
Name: malate dehydrogenase 1
RGD ID: 3072
Description: Enables L-malate dehydrogenase activity and NAD binding activity. Involved in NAD metabolic process; NADH metabolic process; and dicarboxylic acid metabolic process. Predicted to be located in centrosome. Predicted to be active in cytosol. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 88. Orthologous to human MDH1 (malate dehydrogenase 1); PARTICIPATES IN Leigh disease pathway; nicotinamide adenine dinucleotide metabolic pathway; primary hyperoxaluria type 2 pathway; INTERACTS WITH 1-benzylpiperazine; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: cytosolic malate dehydrogenase; malate dehydrogenase 1, NAD (soluble); malate dehydrogenase soluble; malate dehydrogenase, cytoplasmic; malate dehydrogenase, peroxisomal; malate dehydrogenase, soluble; Malate dehydrogenase-like enzyme; Mdhl; MDL1; Mor2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21495,630,625 - 95,645,920 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1495,630,306 - 95,645,925 (-)Ensembl
Rnor_6.014106,378,349 - 106,393,642 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,378,942 - 106,393,670 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014106,449,337 - 106,463,995 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,259,130 - 102,273,788 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,278,343 - 102,292,999 (-)NCBI
Celera1494,639,971 - 94,655,156 (-)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-benzylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,5-hexanedione  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
7H-xanthine  (EXP)
8-Br-cAMP  (ISO)
9H-xanthine  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP)
aldehydo-D-glucose  (EXP,ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (EXP)
choline  (EXP)
chromium trinitrate  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
cocaine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
D-gluconic acid  (EXP)
D-glucose  (EXP,ISO)
deoxycholic acid  (EXP)
Deoxycorticosterone acetate  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dihydroartemisinin  (ISO)
dinophysistoxin 1  (ISO)
dioscin  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (EXP)
glucose  (EXP,ISO)
hydrogen peroxide  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-methionine  (EXP)
leflunomide  (EXP)
malic acid  (ISO)
menthofuran  (EXP)
miconazole  (ISO)
monosodium L-glutamate  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
obeticholic acid  (ISO)
oxaloacetic acid  (ISO)
p-toluidine  (EXP)
paracetamol  (EXP,ISO)
perfluorododecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP)
potassium chloride  (EXP)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
quercetin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium dichromate  (EXP)
streptozocin  (EXP)
sulforaphane  (EXP,ISO)
T-2 toxin  (EXP)
tetrachloromethane  (EXP,ISO)
theophylline  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centrosome  (IEA,ISO)
cytosol  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:3312200   PMID:10075524   PMID:11726686   PMID:14760703   PMID:15489334   PMID:16854843   PMID:17634366   PMID:18614015   PMID:19056867   PMID:22664934   PMID:22871113   PMID:23376485  
PMID:23533145   PMID:24625528   PMID:25340584   PMID:26316108  


Genomics

Comparative Map Data
Mdh1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21495,630,625 - 95,645,920 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1495,630,306 - 95,645,925 (-)Ensembl
Rnor_6.014106,378,349 - 106,393,642 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,378,942 - 106,393,670 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014106,449,337 - 106,463,995 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,259,130 - 102,273,788 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114102,278,343 - 102,292,999 (-)NCBI
Celera1494,639,971 - 94,655,156 (-)NCBICelera
Cytogenetic Map14q22NCBI
MDH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl263,588,609 - 63,607,197 (+)EnsemblGRCh38hg38GRCh38
GRCh38263,588,963 - 63,607,197 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37263,816,097 - 63,834,331 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,669,626 - 63,687,832 (+)NCBINCBI36hg18NCBI36
Build 34263,727,772 - 63,745,979NCBI
Celera263,661,163 - 63,679,336 (+)NCBI
Cytogenetic Map2p15NCBI
HuRef263,556,773 - 63,575,326 (+)NCBIHuRef
CHM1_1263,745,880 - 63,764,431 (+)NCBICHM1_1
Mdh1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391121,506,692 - 21,521,934 (-)NCBIGRCm39mm39
GRCm39 Ensembl1121,506,692 - 21,522,367 (-)Ensembl
GRCm381121,556,692 - 21,571,934 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1121,556,692 - 21,572,367 (-)EnsemblGRCm38mm10GRCm38
MGSCv371121,456,695 - 21,471,937 (-)NCBIGRCm37mm9NCBIm37
MGSCv361121,456,790 - 21,471,832 (-)NCBImm8
Celera1123,704,959 - 23,720,201 (-)NCBICelera
Cytogenetic Map11A3.1NCBI
cM Map1113.89NCBI
Mdh1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542420,706,058 - 20,723,493 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542420,707,765 - 20,723,493 (-)NCBIChiLan1.0ChiLan1.0
MDH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A64,785,132 - 64,803,631 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A64,785,132 - 64,803,631 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A63,658,933 - 63,677,257 (+)NCBIMhudiblu_PPA_v0panPan3
MDH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11063,316,818 - 63,334,556 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1063,316,831 - 63,361,735 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1063,205,783 - 63,223,532 (+)NCBI
ROS_Cfam_1.01064,325,732 - 64,343,477 (+)NCBI
UMICH_Zoey_3.11064,008,394 - 64,026,100 (+)NCBI
UNSW_CanFamBas_1.01064,316,618 - 64,334,341 (+)NCBI
UU_Cfam_GSD_1.01064,609,207 - 64,626,872 (+)NCBI
Mdh1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629219,984,379 - 20,000,470 (-)NCBI
SpeTri2.0NW_0049364918,570,472 - 8,586,914 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MDH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl378,244,999 - 78,440,488 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1378,247,229 - 78,263,085 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2382,274,663 - 82,280,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MDH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11443,406,502 - 43,425,525 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1443,406,499 - 43,425,095 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604568,435,625 - 68,454,293 (+)NCBIVero_WHO_p1.0
Mdh1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247629,884,521 - 9,900,593 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
Mor2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21495,632,978 - 95,633,448 (+)MAPPERmRatBN7.2
Rnor_6.014106,380,703 - 106,381,172NCBIRnor6.0
Rnor_5.014106,451,095 - 106,451,564UniSTSRnor5.0
RGSC_v3.414102,260,888 - 102,261,357UniSTSRGSC3.4
Celera1494,642,325 - 94,642,794UniSTS
Cytogenetic Map14q22UniSTS
RH134361  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21495,631,476 - 95,632,931 (+)MAPPERmRatBN7.2
Rnor_6.014106,379,201 - 106,380,655NCBIRnor6.0
Rnor_5.014106,449,593 - 106,451,047UniSTSRnor5.0
RGSC_v3.414102,259,386 - 102,260,840UniSTSRGSC3.4
Celera1494,640,823 - 94,642,277UniSTS
Cytogenetic Map14q22UniSTS
BE120360  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21495,630,523 - 95,630,634 (+)MAPPERmRatBN7.2
Rnor_6.014106,378,248 - 106,378,358NCBIRnor6.0
Rnor_5.014106,448,640 - 106,448,750UniSTSRnor5.0
RGSC_v3.414102,258,433 - 102,258,543UniSTSRGSC3.4
Celera1494,639,870 - 94,639,980UniSTS
RH 3.4 Map14755.8UniSTS
Cytogenetic Map14q22UniSTS
D2S1567E  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21495,631,516 - 95,632,217 (+)MAPPERmRatBN7.2
Rnor_6.014106,379,241 - 106,379,941NCBIRnor6.0
Rnor_5.014106,449,633 - 106,450,333UniSTSRnor5.0
RGSC_v3.414102,259,426 - 102,260,126UniSTSRGSC3.4
Celera1494,640,863 - 94,641,563UniSTS
Cytogenetic Map14q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat
1582201Sffal2Serum free fatty acids level QTL 240.0002blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)149255388695876975Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:108
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000011429
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 29 9 5
Medium 3 20 57 41 19 41 8 11 65 30 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001316877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_033235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF075574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF093773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC059124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM055335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM081843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM085125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM086546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM108375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FN799180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217819 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011429   ⟹   ENSRNOP00000011429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1495,630,306 - 95,645,925 (-)Ensembl
Rnor_6.0 Ensembl14106,378,942 - 106,393,670 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094321   ⟹   ENSRNOP00000088696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1495,630,306 - 95,640,911 (-)Ensembl
RefSeq Acc Id: NM_001316877   ⟹   NP_001303806
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,630,625 - 95,645,920 (-)NCBI
Rnor_6.014106,378,349 - 106,393,642 (-)NCBI
Celera1494,639,971 - 94,655,156 (-)NCBI
Sequence:
RefSeq Acc Id: NM_033235   ⟹   NP_150238
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21495,630,625 - 95,645,920 (-)NCBI
Rnor_6.014106,378,349 - 106,393,642 (-)NCBI
Rnor_5.014106,449,337 - 106,463,995 (-)NCBI
RGSC_v3.414102,259,130 - 102,273,788 (-)RGD
Celera1494,639,971 - 94,655,156 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_150238   ⟸   NM_033235
- Peptide Label: isoform Mdh1
- UniProtKB: O88989 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001303806   ⟸   NM_001316877
- Peptide Label: isoform Mdh1x
- Sequence:
RefSeq Acc Id: ENSRNOP00000011429   ⟸   ENSRNOT00000011429
RefSeq Acc Id: ENSRNOP00000088696   ⟸   ENSRNOT00000094321

Transcriptome

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

Promoters
RGD ID:13699515
Promoter ID:EPDNEW_R10039
Type:initiation region
Name:Mdh1_1
Description:malate dehydrogenase 1
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_6.014106,393,647 - 106,393,707EPDNEW

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)
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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)
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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
PVG/Seac (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3072 AgrOrtholog
Ensembl Genes ENSRNOG00000008103 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011429 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011429 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.110.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6921518 IMAGE-MGC_LOAD
InterPro L-lactate/malate_DH UniProtKB/Swiss-Prot
  Lactate/malate_DH_C UniProtKB/Swiss-Prot
  Lactate/malate_DH_N UniProtKB/Swiss-Prot
  Lactate_DH/Glyco_Ohase_4_C UniProtKB/Swiss-Prot
  Malate_DH_AS UniProtKB/Swiss-Prot
  Malate_DH_NAD-dep_euk UniProtKB/Swiss-Prot
  Malate_DH_type2 UniProtKB/Swiss-Prot
  NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:24551 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72755 IMAGE-MGC_LOAD
NCBI Gene 24551 ENTREZGENE
PANTHER PTHR23382 UniProtKB/Swiss-Prot
Pfam Ldh_1_C UniProtKB/Swiss-Prot
  Ldh_1_N UniProtKB/Swiss-Prot
PhenoGen Mdh1 PhenoGen
PIRSF Lac_mal_DH UniProtKB/Swiss-Prot
PROSITE MDH UniProtKB/Swiss-Prot
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot
  SSF56327 UniProtKB/Swiss-Prot
TIGRFAMs MalateDH-SF1 UniProtKB/Swiss-Prot
  MDH_euk_cyt UniProtKB/Swiss-Prot
UniProt MDHC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O88585 UniProtKB/Swiss-Prot
  Q6PCV2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-10 Mdh1  malate dehydrogenase 1  Mdh1  malate dehydrogenase 1, NAD (soluble)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Mdh1  malate dehydrogenase 1, NAD (soluble)    malate dehydrogenase 1  Name updated 1299863 APPROVED
2003-05-19 Mdh1  malate dehydrogenase 1  Mor2  malate dehydrogenase, soluble  Data Merged 629477 PROVISIONAL
2003-04-09 Mdh1  malate dehydrogenase 1  Mdhl  Malate dehydrogenase-like enzyme  Symbol and Name updated 629477 APPROVED
2002-08-07 Mor2  malate dehydrogenase, soluble      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Mdhl  Malate dehydrogenase-like enzyme      Symbol and Name status set to approved 70586 APPROVED