Gapdh (glyceraldehyde-3-phosphate dehydrogenase) - Rat Genome Database

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Gene: Gapdh (glyceraldehyde-3-phosphate dehydrogenase) Rattus norvegicus
Analyze
Symbol: Gapdh
Name: glyceraldehyde-3-phosphate dehydrogenase
RGD ID: 2661
Description: Enables several functions, including glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; identical protein binding activity; and peptidyl-cysteine S-nitrosylase activity. Involved in several processes, including cAMP-mediated signaling; gluconeogenesis; and negative regulation of vascular associated smooth muscle cell apoptotic process. Located in several cellular components, including cytosol; microtubule cytoskeleton; and postsynaptic density, intracellular component. Is active in glutamatergic synapse. Used to study Alzheimer's disease and middle cerebral artery infarction. Biomarker of several diseases, including brain glioma; diabetic retinopathy; obesity; oral squamous cell carcinoma; and rheumatic heart disease. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human GAPDH (glyceraldehyde-3-phosphate dehydrogenase); PARTICIPATES IN gluconeogenesis pathway; electron transport chain pathway; Fanconi syndrome pathway; INTERACTS WITH (-)-selegiline; 1,3-dinitrobenzene; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 38 kDa BFA-dependent ADP-ribosylation substrate; BARS-38; Gapd; peptidyl-cysteine S-nitrosylase GAPDH
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gapdh-ps1   Gapdh-ps2   LOC100361351   LOC689831  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24157,962,312 - 157,967,158 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4157,962,343 - 157,966,235 (-)Ensembl
Rnor_6.04157,676,336 - 157,680,322 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,676,595 - 157,679,962 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,693,580 - 224,697,455 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,282,215 - 161,286,090 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1962,857,154 - 62,857,964 (+)NCBI
Celera4146,699,388 - 146,703,263 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-selegiline  (EXP,ISO)
(S)-nicotine  (ISO)
1,10-phenanthroline  (ISO)
1,2-dimethylhydrazine  (ISO)
1,2-naphthoquinone  (ISO)
1,3-dinitrobenzene  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-bromohexadecanoic acid  (EXP)
2-methoxyethanol  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,7-dihydropurine-6-thione  (ISO)
3-bromopyruvic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-nitropropanoic acid  (EXP)
3-phosphoglyceric acid  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
4-tert-Octylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP,ISO)
7-NITROINDAZOLE  (EXP)
9-cis-retinoic acid  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acetic acid  (ISO)
acrolein  (EXP,ISO)
acrylamide  (EXP,ISO)
actinomycin D  (ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-amanitin  (ISO)
alpha-hexachlorocyclohexane  (EXP)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (EXP,ISO)
arsenite(3-)  (EXP)
arsenous acid  (ISO)
ATP  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
beta-D-fructofuranose 1,6-bisphosphate  (EXP)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
boric acid  (ISO)
bromochloroacetic acid  (ISO)
buten-2-one  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
capsaicin  (EXP,ISO)
captan  (ISO)
carbon nanotube  (ISO)
cerium trichloride  (ISO)
chloroacetaldehyde  (EXP)
chloroacetic acid  (EXP)
chloropicrin  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
clozapine  (EXP)
cobalt dichloride  (ISO)
cobalt(2+) sulfate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (EXP,ISO)
cumene hydroperoxide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-fructofuranose 1,6-bisphosphate  (EXP)
D-glucose  (EXP,ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP,ISO)
dichlorine  (EXP)
diethyl maleate  (ISO)
dihydroartemisinin  (ISO)
Diisodecyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
Diosbulbin B  (ISO)
dioxygen  (EXP,ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dizocilpine maleate  (EXP)
dopamine  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
etoposide  (ISO)
fenbuconazole  (ISO)
fentin chloride  (ISO)
ferric ammonium citrate  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
furan  (EXP)
genistein  (EXP)
glafenine  (EXP)
glucose  (EXP,ISO)
glutathione  (EXP,ISO)
glyceraldehyde 3-phosphate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
graphite  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
indometacin  (ISO)
isoflavones  (EXP)
isoniazide  (EXP)
ivermectin  (ISO)
keto-D-fructose 1,6-bisphosphate  (EXP)
L-ascorbic acid  (ISO)
L-ethionine  (EXP)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercaptopurine  (ISO)
methanol  (EXP)
methoxychlor  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (EXP)
N-acetyl-L-cysteine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
NAD zwitterion  (EXP,ISO)
NAD(+)  (EXP,ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nilutamide  (EXP)
nitric oxide  (EXP,ISO)
obeticholic acid  (ISO)
okadaic acid  (ISO)
omeprazole  (EXP)
ozone  (EXP)
p-menthan-3-ol  (ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (EXP)
paraquat  (EXP)
PCB138  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
pirinixic acid  (EXP)
polymyxin B2  (ISO)
potassium dichromate  (EXP)
progesterone  (EXP)
promethazine  (EXP)
prostaglandin A1  (ISO)
purine-6-thiol  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP,ISO)
Rebamipide  (EXP)
resveratrol  (EXP)
retinyl acetate  (ISO)
rimonabant  (ISO)
rotenone  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
Salinomycin  (ISO)
selenium atom  (ISO)
serotonin  (ISO)
serpentine asbestos  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenate  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium dodecyl sulfate  (EXP)
sodium fluoride  (ISO)
sucrose  (ISO)
sunitinib  (ISO)
superoxide  (EXP,ISO)
T-2 toxin  (EXP)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetraethylenepentamine  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenylstannane  (ISO)
trovafloxacin  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
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13. GOA data from the GO Consortium
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23. KEGG
24. Kornberg MD, etal., Nat Cell Biol. 2010 Nov;12(11):1094-100. doi: 10.1038/ncb2114. Epub 2010 Oct 24.
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30. MGD data from the GO Consortium
31. Mi Q, etal., Ann Clin Lab Sci. 2018 Jul;48(4):460-468.
32. Nakajima H, etal., J Biol Chem. 2015 Jun 5;290(23):14493-503. doi: 10.1074/jbc.M114.635607. Epub 2015 Apr 16.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Newman SF, etal., J Neurosci Res. 2007 May 15;85(7):1506-14. doi: 10.1002/jnr.21275.
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38. Pipeline to import KEGG annotations from KEGG into RGD
39. Pipeline to import SMPDB annotations from SMPDB into RGD
40. Qvit N, etal., J Biol Chem. 2016 Jun 24;291(26):13608-21. doi: 10.1074/jbc.M115.711630. Epub 2016 Apr 27.
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42. RGD automated data pipeline
43. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:3796661   PMID:7144574   PMID:10559001   PMID:11487543   PMID:11785981   PMID:12519789   PMID:12753082   PMID:14651853   PMID:14741744   PMID:15159393   PMID:15479637   PMID:15489334  
PMID:15665293   PMID:16170200   PMID:16418269   PMID:16627065   PMID:16751257   PMID:17426931   PMID:17488287   PMID:17634366   PMID:17962088   PMID:18698006   PMID:18720057   PMID:18837965  
PMID:19022411   PMID:19056867   PMID:19075228   PMID:19131967   PMID:19182904   PMID:19190083   PMID:19199708   PMID:19292454   PMID:19470756   PMID:19723108   PMID:19903941   PMID:19940145  
PMID:19946888   PMID:19950597   PMID:20392205   PMID:20458337   PMID:20518697   PMID:21210726   PMID:21257285   PMID:21362503   PMID:21413931   PMID:21482559   PMID:21539824   PMID:21630459  
PMID:21904640   PMID:21988832   PMID:22252379   PMID:22420779   PMID:22832495   PMID:22871113   PMID:23027902   PMID:23071094   PMID:23106098   PMID:23360709   PMID:23376485   PMID:23527007  
PMID:23530063   PMID:23533145   PMID:23979707   PMID:24101517   PMID:24137001   PMID:24507776   PMID:24670206   PMID:26316108   PMID:26748070   PMID:26945066   PMID:28174179   PMID:28259758  
PMID:29476059   PMID:32438512   PMID:33539626   PMID:33546324  


Genomics

Comparative Map Data
Gapdh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24157,962,312 - 157,967,158 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4157,962,343 - 157,966,235 (-)Ensembl
Rnor_6.04157,676,336 - 157,680,322 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,676,595 - 157,679,962 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,693,580 - 224,697,455 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44161,282,215 - 161,286,090 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1962,857,154 - 62,857,964 (+)NCBI
Celera4146,699,388 - 146,703,263 (-)NCBICelera
Cytogenetic Map4q42NCBI
GAPDH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl126,534,512 - 6,538,374 (+)EnsemblGRCh38hg38GRCh38
GRCh38126,534,517 - 6,538,371 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37126,643,683 - 6,647,537 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,513,918 - 6,517,797 (+)NCBINCBI36hg18NCBI36
Build 34126,513,944 - 6,517,797NCBI
Celera128,260,518 - 8,264,397 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef126,497,829 - 6,501,781 (+)NCBIHuRef
CHM1_1126,642,592 - 6,646,544 (+)NCBICHM1_1
Gapdh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396125,138,815 - 125,143,430 (-)NCBIGRCm39mm39
GRCm39 Ensembl6125,138,678 - 125,143,430 (-)Ensembl
GRCm386125,161,852 - 125,166,467 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6125,161,715 - 125,166,467 (-)EnsemblGRCm38mm10GRCm38
MGSCv376125,111,870 - 125,115,601 (-)NCBIGRCm37mm9NCBIm37
MGSCv366125,128,554 - 125,131,222 (-)NCBImm8
Celera6126,831,711 - 126,835,442 (-)NCBICelera
Cytogenetic Map6F2NCBI
cM Map659.32NCBI
Gapdh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,162,467 - 4,166,783 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,162,467 - 4,166,783 (+)NCBIChiLan1.0ChiLan1.0
GAPDH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1126,583,895 - 6,587,729 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl126,583,895 - 6,587,729 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0126,665,218 - 6,669,170 (+)NCBIMhudiblu_PPA_v0panPan3
LOC100688969
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X51,925,654 - 51,926,724 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX42,758,798 - 42,759,848 (+)NCBI
ROS_Cfam_1.0X52,892,500 - 52,893,549 (+)NCBI
UMICH_Zoey_3.1X50,867,280 - 50,868,330 (+)NCBI
UNSW_CanFamBas_1.0X52,198,694 - 52,199,710 (+)NCBI
UU_Cfam_GSD_1.0X52,119,573 - 52,120,589 (+)NCBI
Gapdh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945102,575,598 - 102,580,238 (-)NCBI
SpeTri2.0NW_0049367091,243,149 - 1,247,782 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GAPDH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl564,129,680 - 64,133,991 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1564,129,678 - 64,135,194 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2566,446,302 - 66,449,510 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap5q12-q21NCBI
GAPDH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1116,569,029 - 6,572,877 (+)NCBI
Vero_WHO_p1.0NW_0236660631,653,527 - 1,657,405 (-)NCBI
Gapdh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248603,257,805 - 3,261,736 (+)NCBI

Position Markers
PMC122612P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map10q26UniSTS
Cytogenetic Map18q12.1UniSTS
PMC128021P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map18q12.1UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map10q26UniSTS
Cytogenetic Map5q24UniSTS
Cytogenetic Map6q32UniSTS
PMC133764P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q22UniSTS
Cytogenetic Map9q13UniSTS
Cytogenetic Map16q11UniSTS
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map2q34UniSTS
Cytogenetic Map10q26UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map18q12.1UniSTS
PMC15575P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map18q12.1UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map2q42UniSTS
Cytogenetic Map11q22UniSTS
PMC164515P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map6q32UniSTS
PMC186377P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map8q22UniSTS
PMC26839P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map16q11UniSTS
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map15q21UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map18q12.1UniSTS
PMC316856P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map16q11UniSTS
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map18q12.1UniSTS
PMC327192P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map19p11UniSTS
PMC329392P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map18q12.1UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map15q21UniSTS
Cytogenetic Map2q42UniSTS
Cytogenetic Map10q32.1UniSTS
PMC128235P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map8q22UniSTS
Cytogenetic Map18q12.1UniSTS
Cytogenetic Map11q22UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map13q22UniSTS
Cytogenetic Map19p11UniSTS
Cytogenetic Map15q21UniSTS
Cytogenetic Map7q13UniSTS
Cytogenetic Map2q42UniSTS
Cytogenetic Map3q21UniSTS
RH140227  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,961,933 - 157,962,127 (+)MAPPERmRatBN7.2
Rnor_6.04157,675,972 - 157,676,165NCBIRnor6.0
Rnor_5.04224,693,156 - 224,693,349UniSTSRnor5.0
RGSC_v3.44161,281,791 - 161,281,984UniSTSRGSC3.4
Celera4146,698,964 - 146,699,157UniSTS
RH 3.4 Map41005.8UniSTS
Cytogenetic Map4q42UniSTS
PMC193571P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q33UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map10q32.1UniSTS
PMC104479P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X55,897,275 - 55,897,778NCBIRnor5.0
Rnor_5.01207,898,087 - 207,898,589NCBIRnor5.0
Rnor_5.01208,042,287 - 208,042,789NCBIRnor5.0
RGSC_v3.4X93,852,831 - 93,853,333UniSTSRGSC3.4
RGSC_v3.41189,771,940 - 189,772,441UniSTSRGSC3.4
CeleraX72,115,994 - 72,116,496UniSTS
Celera1182,631,486 - 182,631,987UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map1q37UniSTS
PMC112827P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X55,897,275 - 55,897,396NCBIRnor5.0
Rnor_5.01207,898,087 - 207,898,207NCBIRnor5.0
Rnor_5.01208,042,287 - 208,042,407NCBIRnor5.0
RGSC_v3.4X93,852,831 - 93,852,951UniSTSRGSC3.4
RGSC_v3.41189,771,940 - 189,772,059UniSTSRGSC3.4
CeleraX72,115,994 - 72,116,114UniSTS
Celera1182,631,486 - 182,631,605UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map1q37UniSTS
PMC115884P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X55,897,276 - 55,897,582NCBIRnor5.0
Rnor_5.01207,898,088 - 207,898,393NCBIRnor5.0
Rnor_5.01208,042,288 - 208,042,593NCBIRnor5.0
RGSC_v3.4X93,852,832 - 93,853,137UniSTSRGSC3.4
RGSC_v3.41189,771,941 - 189,772,245UniSTSRGSC3.4
CeleraX72,115,995 - 72,116,300UniSTS
Celera1182,631,487 - 182,631,791UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map1q37UniSTS
PMC21468P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X55,897,276 - 55,897,638NCBIRnor5.0
Rnor_5.01207,898,088 - 207,898,449NCBIRnor5.0
Rnor_5.01208,042,288 - 208,042,649NCBIRnor5.0
RGSC_v3.4X93,852,832 - 93,853,193UniSTSRGSC3.4
RGSC_v3.41189,771,941 - 189,772,301UniSTSRGSC3.4
CeleraX72,115,995 - 72,116,356UniSTS
Celera1182,631,487 - 182,631,847UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map4q42UniSTS
Cytogenetic Map1q37UniSTS
PMC266773P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01207,898,088 - 207,898,449NCBIRnor5.0
Rnor_5.0X55,897,276 - 55,897,638NCBIRnor5.0
Rnor_5.01208,042,288 - 208,042,649NCBIRnor5.0
RGSC_v3.41189,771,941 - 189,772,301UniSTSRGSC3.4
RGSC_v3.4X93,852,832 - 93,853,193UniSTSRGSC3.4
Celera1182,631,487 - 182,631,847UniSTS
CeleraX72,115,995 - 72,116,356UniSTS
Cytogenetic Map1q37UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map4q42UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:48
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000050443
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 35 12 12 12 8 11 47 22 13 8
Medium 3 8 45 29 19 29 27 13 28 11
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: NM_017008   ⟹   NP_058704
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24157,962,358 - 157,966,233 (-)NCBI
Rnor_6.04157,676,396 - 157,680,271 (-)NCBI
Rnor_5.04224,693,580 - 224,697,455 (-)NCBI
RGSC_v3.44161,282,215 - 161,286,090 (-)RGD
Celera4146,699,388 - 146,703,263 (-)RGD
Sequence:
RefSeq Acc Id: XM_039107008   ⟹   XP_038962936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24157,962,312 - 157,967,158 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058704   ⟸   NM_017008
- UniProtKB: P04797 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_038962936   ⟸   XM_039107008
- Peptide Label: isoform X1
Protein Domains
Gp_dh_N

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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:2661 AgrOrtholog
Ensembl Genes ENSRNOG00000018630 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000040878 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000050443 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6919611 IMAGE-MGC_LOAD
  IMAGE:7321006 IMAGE-MGC_LOAD
InterPro GlycerAld/Erythrose_P_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GlycerAld_3-P_DH_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GlycerAld_3-P_DH_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GlycerAld_3-P_DH_NAD(P)-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glyceraldehyde-3-P_DH_1 UniProtKB/Swiss-Prot
  NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24383 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105280 IMAGE-MGC_LOAD
  MGC:72650 IMAGE-MGC_LOAD
NCBI Gene 24383 ENTREZGENE
PANTHER PTHR10836 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Gp_dh_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Gp_dh_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gapdh PhenoGen
PIRSF GAP_DH UniProtKB/Swiss-Prot
PRINTS G3PDHDRGNASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GAPDH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Gp_dh_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs GAPDH-I UniProtKB/Swiss-Prot
UniProt G3P_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  P97617_RAT UniProtKB/TrEMBL
  Q0QEU1_RAT UniProtKB/TrEMBL
  Q8K4T7_RAT UniProtKB/TrEMBL
  Q8K4T8_RAT UniProtKB/TrEMBL
UniProt Secondary P09328 UniProtKB/Swiss-Prot
  Q5M916 UniProtKB/Swiss-Prot
  Q9QWU4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-02-01 Gapdh    Gapd  glyceraldehyde-3-phosphate dehydrogenase  Symbol updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2002-06-10 Gapd  Glyceraldehyde-3-phosphate dehydrogenase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in atria and ventricles of the heart 625420
gene_expression expressed in all tissues 632774
gene_protein 333 amino acids 632774