Aldh1a1 (aldehyde dehydrogenase 1 family, member A1) - Rat Genome Database

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Gene: Aldh1a1 (aldehyde dehydrogenase 1 family, member A1) Rattus norvegicus
Analyze
Symbol: Aldh1a1
Name: aldehyde dehydrogenase 1 family, member A1
RGD ID: 2087
Description: Enables benzaldehyde dehydrogenase (NAD+) activity; identical protein binding activity; and retinal dehydrogenase activity. Involved in several processes, including estrous cycle; response to estradiol; and retinoic acid metabolic process. Located in cytoplasm and nucleus. Orthologous to human ALDH1A1 (aldehyde dehydrogenase 1 family member A1); PARTICIPATES IN retinoic acid metabolic pathway; cyclophosphamide pharmacodynamics pathway; cyclophosphamide pharmacokinetics pathway; INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ahd2; Aldehyde dehydrogenase 1; Aldehyde dehydrogenase 1 subfamily A1; Aldehyde dehydrogenase 1, subfamily A1; aldehyde dehydrogenase 1A1; aldehyde dehydrogenase 2; aldehyde dehydrogenase family 1 member A1; aldehyde dehydrogenase family 1, member A1; aldehyde dehydrogenase family 1, subfamily A1; aldehyde dehydrogenase, cytosolic; ALDH-E1; Aldh1; Aldh2; ALHDII; LOC103695056; RALDH 1; ralDH1; retinal dehydrogenase 1; uncharacterized LOC103695056
RGD Orthologs
Human
Mouse
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
mRatBN7.21218,000,470 - 218,152,962 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1218,042,127 - 218,152,961 (+)Ensembl
Rnor_6.01238,222,689 - 238,264,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1238,222,521 - 238,264,330 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01245,340,587 - 245,562,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,731,675 - 223,773,285 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,895,697 - 223,937,307 (+)NCBI
Celera1215,379,207 - 215,421,068 (+)NCBICelera
Cytogenetic Map1q51NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(20S)-ginsenoside Rg3  (ISO)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (ISO)
1-nitropropane  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-diaminotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-diaminotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-[cyclohexyl(oxo)methyl]-3,6,7,11b-tetrahydro-1H-pyrazino[2,1-a]isoquinolin-4-one  (EXP)
2-acetamidofluorene  (EXP)
2-amino-4,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-hexenal  (ISO)
2-nitro-p-phenylenediamine  (EXP)
2-nitrofluorene  (EXP)
2-nitropropane  (EXP)
22-Hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4'-hydroxyacetophenone  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(diethylamino)benzaldehyde  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-acetylaminofluorene  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-dimethylaminocinnamaldehyde  (ISO)
4-hydroperoxycyclophosphamide  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitro-1,2-phenylenediamine  (EXP)
4-nitrophenol  (ISO)
4-nitrophenyl acetate  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-Hydroxythalidomide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
7H-xanthine  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinal  (EXP,ISO)
9H-xanthine  (ISO)
acetaldehyde  (EXP,ISO)
acetamide  (EXP)
acetic acid  (ISO)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
adenosine 5'-monophosphate  (ISO)
aflatoxin B1  (EXP,ISO)
Aldophosphamide  (ISO)
all-trans-retinal  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
allopurinol  (EXP)
alpha-hexachlorocyclohexane  (EXP)
amiodarone  (EXP)
amitriptyline  (EXP)
amphetamine  (ISO)
anthracen-2-amine  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP)
arsenous acid  (ISO)
auramine O  (ISO)
azathioprine  (EXP)
bacitracin  (EXP)
benzaldehyde  (EXP,ISO)
benzbromarone  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzophenone  (EXP)
benzyl isothiocyanate  (ISO)
beta-naphthoflavone  (EXP)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
butylated hydroxyanisole  (ISO)
Butylbenzyl phthalate  (ISO)
butyric acid  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcitriol  (ISO)
captan  (ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
carboplatin  (ISO)
casticin  (ISO)
chloroform  (EXP)
chlorohydrocarbon  (EXP)
chlorpromazine  (ISO)
chlorpyrifos  (ISO)
ciglitazone  (EXP)
cimetidine  (ISO)
ciprofibrate  (EXP,ISO)
ciprofloxacin  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP,ISO)
clomipramine  (EXP)
clothianidin  (EXP)
clozapine  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
coumarin  (EXP)
CU-O LINKAGE  (ISO)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cyproconazole  (EXP,ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
Diallyl sulfide  (EXP,ISO)
diallyl trisulfide  (ISO)
diamminedichloroplatinum  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dichlorvos  (EXP)
dicrotophos  (ISO)
diethyl maleate  (ISO)
diethyl phthalate  (ISO)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
dimethyl sulfoxide  (EXP)
dioxygen  (ISO)
disulfiram  (EXP,ISO)
diuron  (EXP)
doxorubicin  (ISO)
Echimidine  (EXP)
endosulfan  (EXP)
enilconazole  (EXP,ISO)
epoxiconazole  (EXP)
erythromycin estolate  (EXP)
ethanol  (EXP,ISO)
ethoxyquin  (EXP,ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
felbamate  (EXP)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
furosemide  (EXP)
gadodiamide hydrate  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glutathione  (EXP)
graphene oxide  (ISO)
Heliotrine  (EXP)
hexanal  (ISO)
hydrogen peroxide  (ISO)
imipramine  (EXP)
indirubin-3'-monoxime  (ISO)
indole-3-methanol  (EXP,ISO)
irinotecan  (ISO)
ketoconazole  (EXP)
L-ethionine  (EXP)
lapatinib  (ISO)
Lasiocarpine  (EXP)
lead diacetate  (ISO)
Licochalcone B  (ISO)
limonin  (ISO)
lipopolysaccharide  (ISO)
magnesium atom  (EXP)
magnesium dichloride  (EXP)
malonaldehyde  (ISO)
manganese(II) chloride  (EXP)
menadione  (ISO)
metformin  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
methylparaben  (ISO)
miconazole  (EXP)
Monobutylphthalate  (ISO)
monosodium L-glutamate  (ISO)
monuron  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
NAD zwitterion  (ISO)
NAD(+)  (ISO)
naphthalene  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel subsulfide  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
nitroglycerin  (EXP)
non-2-enal  (ISO)
ochratoxin A  (EXP)
octadecanoic acid  (ISO)
okadaic acid  (ISO)
oleic acid  (ISO)
oltipraz  (ISO)
omeprazole  (EXP)
orphenadrine  (EXP)
p-toluidine  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phencyclidine  (ISO)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
phenytoin  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
prochloraz  (EXP)
progesterone  (ISO)
propanal  (EXP,ISO)
propiconazole  (EXP,ISO)
pyrazinecarboxamide  (EXP)
pyrogallol  (ISO)
quartz  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
Salinomycin  (ISO)
senecionine  (EXP)
Senkirkine  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP)
Soman  (EXP)
spironolactone  (ISO)
streptozocin  (EXP)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sulindac  (EXP)
T-2 toxin  (EXP)
tacrolimus hydrate  (ISO)
tanespimycin  (ISO)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thiacloprid  (EXP,ISO)
thioacetamide  (EXP)
Thiotepa  (ISO)
titanium dioxide  (EXP,ISO)
toluene  (EXP)
transplatin  (ISO)
triadimefon  (EXP)
tributylstannane  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
trimethylarsine oxide  (EXP)
triphenyl phosphate  (EXP)
troglitazone  (EXP)
trovafloxacin  (EXP)
Tungsten carbide  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (EXP)
vinclozolin  (EXP)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IEA,ISO,ISS)
cytoplasm  (IDA)
cytosol  (ISO,ISS)
nucleus  (IDA)
synapse  (IEA,ISO,ISS)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Bateman OA, etal., Biochemistry. 2003 Apr 22;42(15):4349-56.
2. Bhat PV, etal., Gene 1995 Dec 12;166(2):303-6.
3. Brodeur H, etal., Biochem Cell Biol. 2006 Oct;84(5):799-804.
4. Choudhary S, etal., Invest Ophthalmol Vis Sci. 2005 Jan;46(1):259-67.
5. Fujiwara K, etal., Endocr J. 2008 Mar;55(1):91-6. Epub 2008 Jan 17.
6. Fujiwara K, etal., Med Mol Morphol. 2008 Sep;41(3):126-31. Epub 2008 Sep 20.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Guimond J, etal., Biochim Biophys Acta 2002 Dec 12;1579(2-3):81-91.
10. Kathmann EC and Lipsky JJ, Adv Exp Med Biol 1997;414:69-72.
11. Kathmann EC and Lipsky JJ, Biochem Biophys Res Commun 1997 Jul 18;236(2):527-31.
12. Kathmann EC, etal., Biochemistry. 2000 Sep 12;39(36):11170-6.
13. KEGG
14. Kiefer FW, etal., Nat Med. 2012 Jun;18(6):918-25. doi: 10.1038/nm.2757.
15. Labrecque J, etal., Biochem J. 1995 Jan 15;305 ( Pt 2):681-4.
16. Marlier A and Gilbert T, Gene Expr Patterns. 2004 Dec;5(2):179-85.
17. MGD data from the GO Consortium
18. Moon KH, etal., FEBS Lett. 2007 Aug 21;581(21):3967-72. Epub 2007 Jul 25.
19. Napoli JL Biochim Biophys Acta. 2012 Jan;1821(1):152-67. Epub 2011 May 19.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nishiguchi M, etal., Alcohol Alcohol. 2002 Jan-Feb;37(1):9-12.
22. Ogura Y, etal., Life Sci. 2004 Feb 6;74(12):1519-28.
23. Ogura Y, etal., Life Sci. 2005 Oct 14;77(22):2804-13.
24. Pappas P, etal., Eur J Drug Metab Pharmacokinet. 1998 Oct-Dec;23(4):461-7.
25. Penzes P, etal., Gene 1997 Jun 3;191(2):167-72.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Pipeline to import SMPDB annotations from SMPDB into RGD
28. RGD automated data pipeline
29. RGD automated import pipeline for gene-chemical interactions
30. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
31. Walsh N, etal., Proteome Sci. 2009 Feb 14;7:3.
32. Wang C, etal., J Biol Chem. 2011 Feb 25;286(8):6542-53. Epub 2010 Dec 7.
33. Yoon M, etal., Toxicol Sci. 2006 Feb;89(2):386-98. Epub 2005 Nov 16.
34. Zhai Y, etal., J Cell Physiol. 2001 Feb;186(2):220-32.
Additional References at PubMed
PMID:224930   PMID:4015840   PMID:10191271   PMID:11876656   PMID:12610736   PMID:12808103   PMID:12851412   PMID:15489334   PMID:15682487   PMID:16207763   PMID:16611695   PMID:17180597  
PMID:17257171   PMID:17497177   PMID:18971422   PMID:19056867   PMID:19199708   PMID:19671997   PMID:22170038   PMID:23028851   PMID:23376485   PMID:23533145   PMID:25450233   PMID:27618414  
PMID:28392548   PMID:33400378  


Genomics

Comparative Map Data
Aldh1a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21218,000,470 - 218,152,962 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1218,042,127 - 218,152,961 (+)Ensembl
Rnor_6.01238,222,689 - 238,264,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1238,222,521 - 238,264,330 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01245,340,587 - 245,562,970 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,731,675 - 223,773,285 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,895,697 - 223,937,307 (+)NCBI
Celera1215,379,207 - 215,421,068 (+)NCBICelera
Cytogenetic Map1q51NCBI
ALDH1A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl972,900,671 - 73,080,442 (-)EnsemblGRCh38hg38GRCh38
GRCh38972,900,671 - 72,953,053 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37975,515,587 - 75,567,969 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36974,705,407 - 74,757,789 (-)NCBINCBI36hg18NCBI36
Build 34972,745,141 - 72,797,523NCBI
Celera946,088,447 - 46,140,830 (-)NCBI
Cytogenetic Map9q21.13NCBI
HuRef945,338,144 - 45,390,773 (-)NCBIHuRef
CHM1_1975,662,616 - 75,715,255 (-)NCBICHM1_1
Aldh1a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391920,469,947 - 20,620,827 (+)NCBIGRCm39mm39
GRCm39 Ensembl1920,470,079 - 20,620,829 (+)Ensembl
GRCm381920,492,583 - 20,643,463 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1920,492,715 - 20,643,465 (+)EnsemblGRCm38mm10GRCm38
MGSCv371920,676,472 - 20,717,952 (+)NCBIGRCm37mm9NCBIm37
MGSCv361920,669,079 - 20,710,559 (+)NCBImm8
Celera1921,323,202 - 21,366,435 (+)NCBICelera
Cytogenetic Map19BNCBI
cM Map1913.91NCBI
ALDH1A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1971,680,352 - 71,859,144 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl971,680,890 - 71,814,085 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0951,737,305 - 51,916,648 (+)NCBIMhudiblu_PPA_v0panPan3
ALDH1A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1184,940,411 - 84,994,789 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl184,940,411 - 84,994,789 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha185,406,217 - 85,460,597 (+)NCBI
ROS_Cfam_1.0185,390,369 - 85,444,756 (+)NCBI
UMICH_Zoey_3.1185,159,477 - 85,213,817 (+)NCBI
UNSW_CanFamBas_1.0184,862,384 - 84,917,606 (+)NCBI
UU_Cfam_GSD_1.0185,621,439 - 85,676,732 (+)NCBI
Aldh1a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947132,159,211 - 132,303,931 (+)NCBI
SpeTri2.0NW_0049365038,869,073 - 8,953,726 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ALDH1A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,161,296 - 226,217,312 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,163,347 - 226,217,342 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21252,778,605 - 252,808,516 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ALDH1A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11283,949,529 - 84,092,452 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1283,949,399 - 84,009,003 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603872,378,038 - 72,569,020 (-)NCBIVero_WHO_p1.0
Aldh1a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624811505,297 - 563,795 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94633  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21218,152,697 - 218,152,876 (+)MAPPERmRatBN7.2
Rnor_6.01238,264,117 - 238,264,295NCBIRnor6.0
Rnor_5.01245,562,706 - 245,562,884UniSTSRnor5.0
RGSC_v3.41223,773,021 - 223,773,199UniSTSRGSC3.4
Celera1215,420,804 - 215,420,982UniSTS
Cytogenetic Map1q51UniSTS
D1Bda57  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21218,152,592 - 218,152,800 (+)MAPPERmRatBN7.2
Rnor_6.01238,264,012 - 238,264,219NCBIRnor6.0
Rnor_5.01245,562,601 - 245,562,808UniSTSRnor5.0
RGSC_v3.41223,772,916 - 223,773,123UniSTSRGSC3.4
Celera1215,420,699 - 215,420,906UniSTS
Cytogenetic Map1q51UniSTS
RH137275  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21218,152,663 - 218,152,850 (+)MAPPERmRatBN7.2
Rnor_6.01238,264,083 - 238,264,269NCBIRnor6.0
Rnor_5.01245,562,672 - 245,562,858UniSTSRnor5.0
RGSC_v3.41223,772,987 - 223,773,173UniSTSRGSC3.4
Celera1215,420,770 - 215,420,956UniSTS
Cytogenetic Map1q51UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1199368955224569684Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1173108781218108781Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1174133260219133260Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1144267353222987745Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1181133855226133855Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1198211513225126682Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1188377360224054420Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1207702246228581766Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1184550676229550676Rat
634312Bp143Blood pressure QTL 14330.0002arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1182623426219932796Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
634340Hcar5Hepatocarcinoma resistance QTL 58liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1214537555226660468Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1176550523221550523Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1185145134221264292Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1102813953218753816Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
1558658Bw59Body weight QTL 593.50.0003body mass (VT:0001259)body weight (CMO:0000012)1178784622223784622Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1181829673224569684Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1156677124218753816Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1185356336231689108Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1151162766225824951Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
61403Niddm4Non-insulin dependent diabetes mellitus QTL 4blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1206329708222745518Rat
5508828Leukc3Leukocyte quantity QTL 3eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)1218108584224054420Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1180359209218108781Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1149448574221264292Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
10059590Kidm44Kidney mass QTL 443.420.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1191033875236033875Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1176869060221869060Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:208
Count of miRNA genes:139
Interacting mature miRNAs:162
Transcripts:ENSRNOT00000024000
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 4 2
Medium 3 14 26 23 3 23 8 11 31 31 38 11 8
Low 29 27 14 13 14 43 1
Below cutoff 4 4 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024000   ⟹   ENSRNOP00000024000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1218,110,834 - 218,152,961 (+)Ensembl
Rnor_6.0 Ensembl1238,222,521 - 238,264,330 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112107   ⟹   ENSRNOP00000090793
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1218,042,127 - 218,152,961 (+)Ensembl
RefSeq Acc Id: NM_022407   ⟹   NP_071852
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,111,085 - 218,152,962 (+)NCBI
Rnor_6.01238,222,689 - 238,264,381 (+)NCBI
Rnor_5.01245,340,587 - 245,562,970 (+)NCBI
RGSC_v3.41223,731,675 - 223,773,285 (+)RGD
Celera1215,379,207 - 215,421,068 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093858   ⟹   XP_038949786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,000,471 - 218,152,901 (+)NCBI
RefSeq Acc Id: XM_039093900   ⟹   XP_038949828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,000,477 - 218,152,901 (+)NCBI
RefSeq Acc Id: XM_039093931   ⟹   XP_038949859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,000,470 - 218,152,901 (+)NCBI
RefSeq Acc Id: XM_039093955   ⟹   XP_038949883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,043,987 - 218,152,901 (+)NCBI
RefSeq Acc Id: XM_039093967   ⟹   XP_038949895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21218,000,574 - 218,152,901 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_071852   ⟸   NM_022407
- UniProtKB: P51647 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024000   ⟸   ENSRNOT00000024000
RefSeq Acc Id: XP_038949859   ⟸   XM_039093931
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949786   ⟸   XM_039093858
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949828   ⟸   XM_039093900
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949895   ⟸   XM_039093967
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949883   ⟸   XM_039093955
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000090793   ⟸   ENSRNOT00000112107
Protein Domains
Aldedh

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 245537100 245537101 C T snv WN/N (KNAW), LE/Stm (KyushuU), LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 218126865 218126866 C T snv FXLE18/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), WN/N (2020), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF2B/Stm (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 238238467 238238468 C T snv WN/N (MCW), FXLE18/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), WN/N (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF1C/Stm (2019)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 223747458 223747459 C T snv LE/Stm (KNAW), WN/N (KNAW), LE/Stm (ICL), LCR/2Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), HCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2087 AgrOrtholog
Ensembl Genes ENSRNOG00000017619 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024000 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024000 UniProtKB/TrEMBL
Gene3D-CATH 3.40.309.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.605.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6921926 IMAGE-MGC_LOAD
InterPro Ald_DH/histidinol_DH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_DH_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_DH_CS_CYS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_DH_CS_GLU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ald_DH_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Aldehyde_DH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24188 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72648 IMAGE-MGC_LOAD
NCBI Gene 24188 ENTREZGENE
Pfam Aldedh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ALDH1A1 RGD
PhenoGen Aldh1a1 PhenoGen
PROSITE ALDEHYDE_DEHYDR_CYS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALDEHYDE_DEHYDR_GLU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53720 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHP1_RAT UniProtKB/TrEMBL
  AL1A1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O09184 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Aldh1a1  aldehyde dehydrogenase 1 family, member A1  LOC103695056  uncharacterized LOC103695056  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103695056  uncharacterized LOC103695056      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-26 Aldh1a1  aldehyde dehydrogenase 1 family, member A1  Aldh1a1  aldehyde dehydrogenase family 1, subfamily A1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Aldh1a1  aldehyde dehydrogenase family 1, subfamily A1  Aldh1a1  aldehyde dehydrogenase 1 family, member A1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-12 Aldh1a1  aldehyde dehydrogenase 1 family, member A1  Aldh1a1  aldehyde dehydrogenase family 1, member A1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Aldh1a1  aldehyde dehydrogenase family 1, member A1     Aldehyde dehydrogenase 1, subfamily A1  Name updated 629478 APPROVED
2001-06-12 Aldh1  Aldehyde dehydrogenase 2      Symbol and Name withdrawn 62408 WITHDRAWN
2001-06-12 Aldh1a1  Aldehyde dehydrogenase 1, subfamily A1      Symbol and Name updated to reflect Human and Mouse nomenclature 62408 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains high luciferase activity is seen in the cloned 1360-bp promoter, mutation in the CCAAT box (-72 to -68) abolished the luciferase activity, octamer (Oct)-binding site (-56 to -49) and the CCAAT-binding proteins help in the regulation of the gene 628383
gene_domains high luciferase activity is seen in the cloned 1360-bp promoter, mutation in the CCAAT box (-72 to -68) abolished the luciferase activity, octamer (Oct)-binding site (-56 to -49) and the CCAAT-binding proteins help in the regulation of the gene 628400
gene_expression high levels are observed in developing kidneys and in stomach and intestine but weakly expressed in the liver 628383
gene_expression high levels are observed in developing kidneys and in stomach and intestine but weakly expressed in the liver 628400
gene_function catalyzes the oxidation of retinal to retinoic acid 628383
gene_function catalyzes the oxidation of retinal to retinoic acid 628400
gene_process involved in the prduction of RA required for proper differentiation of the epithelia 628383
gene_process involved in the prduction of RA required for proper differentiation of the epithelia 628400