Acaca (acetyl-CoA carboxylase alpha) - Rat Genome Database

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Gene: Acaca (acetyl-CoA carboxylase alpha) Rattus norvegicus
Analyze
Symbol: Acaca
Name: acetyl-CoA carboxylase alpha
RGD ID: 621248
Description: Enables acetyl-CoA carboxylase activity; biotin binding activity; and kinase binding activity. Involved in fatty acid biosynthetic process; response to drug; and response to organic cyclic compound. Predicted to be located in actin cytoskeleton; cytosol; and fibrillar center. Used to study fatty liver disease. Orthologous to human ACACA (acetyl-CoA carboxylase alpha); PARTICIPATES IN fatty acid biosynthetic pathway; Leigh disease pathway; malonic aciduria pathway; INTERACTS WITH (S)-nicotine; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Acac; ACC-alpha; ACC1; acetyl-CoA carboxylase 1; acetyl-coenzyme A carboxylase; acetyl-Coenzyme A carboxylase alpha
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,014,261 - 69,276,453 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1069,014,170 - 69,276,457 (+)Ensembl
Rnor_6.01071,519,392 - 71,719,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1071,536,533 - 71,719,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,431,885 - 71,630,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41072,483,772 - 72,677,134 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11072,498,141 - 72,691,504 (+)NCBI
Celera1068,011,070 - 68,201,435 (+)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (EXP)
1,2,3,4,6-pentakis-O-galloyl-beta-D-glucose  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2,2-tetramine  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-tert-Octylphenol  (EXP)
5-(2-chloroethyl)-4-methylthiazole  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
6-propyl-2-thiouracil  (EXP)
9-oxononanoic acid  (EXP)
acadesine  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
AICA ribonucleotide  (EXP,ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-linolenic acid  (EXP)
alpha-pinene  (ISO)
amiodarone  (EXP,ISO)
amlexanox  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azoxystrobin  (EXP,ISO)
benzbromarone  (EXP)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
benzylpenicillin  (ISO)
beta-D-glucosamine  (ISO)
bexarotene  (EXP)
bezafibrate  (ISO)
biguanides  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
C60 fullerene  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (ISO)
capsazepine  (ISO)
carbendazim  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
Chicoric acid  (EXP)
chloroethene  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (EXP)
cholesterol  (ISO)
choline  (EXP,ISO)
cis-caffeic acid  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofazimine  (EXP)
clofibrate  (EXP)
cobalt dichloride  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
corticosterone  (EXP)
cortisol  (ISO)
crizotinib  (ISO)
curcumin  (EXP,ISO)
cyanocob(III)alamin  (EXP)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
DDE  (ISO)
deoxypodophyllotoxin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
diethyl maleate  (ISO)
Diosbulbin B  (ISO)
dioxygen  (ISO)
dorsomorphin  (EXP,ISO)
doxorubicin  (ISO)
duvoglustat  (ISO)
endosulfan  (EXP)
erlotinib hydrochloride  (ISO)
erythromycin A  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
fipronil  (ISO)
flavonoids  (EXP)
fluoxetine  (EXP)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
fructose  (EXP,ISO)
furan  (EXP)
gadolinium trichloride  (ISO)
Ganoderic acid A  (ISO)
Gastrodin  (ISO)
geraniol  (ISO)
glafenine  (EXP)
glucose  (EXP,ISO)
glycine betaine  (EXP)
glyphosate  (ISO)
guggulsterone  (ISO)
GW 4064  (ISO)
hexadecanoic acid  (ISO)
Honokiol  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
isoprenaline  (EXP,ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-ethionine  (EXP)
L-methionine  (EXP,ISO)
linoleic acid  (EXP)
lipopolysaccharide  (ISO)
liraglutide  (ISO)
lithocholic acid  (ISO)
lovastatin  (ISO)
mangiferin  (EXP)
metformin  (EXP,ISO)
methapyrilene  (EXP,ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
microcystin-LR  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (ISO)
myriocin  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
naringin  (ISO)
nefazodone  (EXP)
niclosamide  (ISO)
nicotinamide  (EXP,ISO)
nicotine  (EXP)
nilotinib  (ISO)
nimesulide  (EXP)
obeticholic acid  (ISO)
olanzapine  (ISO)
olaparib  (ISO)
oleic acid  (ISO)
omeprazole  (EXP)
orlistat  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
penconazole  (ISO)
perfluorobutanesulfonic acid  (ISO)
perfluorobutyric acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenformin  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
platycodin D  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propamocarb  (ISO)
protein kinase inhibitor  (ISO)
puerarin  (ISO)
pyruvic acid  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
raffinose  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rimonabant  (ISO)
rotenone  (EXP)
rubimaillin  (ISO)
ruthenium red  (ISO)
S-allylcysteine  (ISO)
SB 431542  (ISO)
scopoletin  (EXP)
silibinin  (ISO)
sirtinol  (ISO)
sodium arsenite  (EXP,ISO)
splitomicin  (ISO)
steviol  (ISO)
streptozocin  (EXP)
sucrose  (EXP,ISO)
sulindac  (ISO)
sunitinib  (ISO)
taurine  (EXP,ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
tetrathiomolybdate(2-)  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trametinib  (ISO)
trans-caffeic acid  (ISO)
triacsin C  (ISO)
triazines  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
triclocarban  (EXP)
triolein  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (ISO)
trovafloxacin  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
ursolic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vemurafenib  (ISO)
vinclozolin  (EXP)
WIN 55212-2  (ISO)
zidovudine  (ISO)
zinc atom  (EXP,ISO)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
actin cytoskeleton  (IEA,ISO)
cytosol  (IEA,ISO,ISS)
fibrillar center  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:1974251   PMID:2567668   PMID:2573562   PMID:2900138   PMID:7910165   PMID:8954960   PMID:16216881   PMID:16396499   PMID:17210641   PMID:17218081   PMID:17956983   PMID:18280001  
PMID:18381287   PMID:18534630   PMID:18614015   PMID:19618481   PMID:20457939   PMID:20952656   PMID:23376485   PMID:23479225   PMID:26976583   PMID:27352290   PMID:28993954   PMID:29899443  


Genomics

Comparative Map Data
Acaca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,014,261 - 69,276,453 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1069,014,170 - 69,276,457 (+)Ensembl
Rnor_6.01071,519,392 - 71,719,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1071,536,533 - 71,719,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,431,885 - 71,630,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41072,483,772 - 72,677,134 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11072,498,141 - 72,691,504 (+)NCBI
Celera1068,011,070 - 68,201,435 (+)NCBICelera
Cytogenetic Map10q26NCBI
ACACA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1737,084,992 - 37,406,836 (-)EnsemblGRCh38hg38GRCh38
GRCh381737,084,992 - 37,406,836 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371735,441,927 - 35,766,927 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361732,516,040 - 32,841,015 (-)NCBINCBI36hg18NCBI36
Build 341732,516,039 - 32,841,015NCBI
Celera1732,264,387 - 32,589,361 (-)NCBI
Cytogenetic Map17q12NCBI
HuRef1731,378,027 - 31,583,939 (-)NCBIHuRef
HuRef1731,594,734 - 31,704,859 (-)NCBIHuRef
CHM1_11735,476,555 - 35,798,374 (-)NCBICHM1_1
Acaca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391184,020,461 - 84,292,477 (+)NCBIGRCm39mm39
GRCm39 Ensembl1184,020,498 - 84,292,477 (+)Ensembl
GRCm381184,129,635 - 84,401,651 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1184,129,672 - 84,401,651 (+)EnsemblGRCm38mm10GRCm38
MGSCv371184,008,940 - 84,215,153 (+)NCBIGRCm37mm9NCBIm37
MGSCv361184,011,659 - 84,215,878 (+)NCBImm8
Celera1193,804,708 - 94,012,980 (+)NCBICelera
Cytogenetic Map11CNCBI
Acaca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955451600,254 - 909,892 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955451679,033 - 909,892 (+)NCBIChiLan1.0ChiLan1.0
ACACA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11719,969,199 - 20,297,651 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1719,969,205 - 20,297,651 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01719,670,114 - 19,998,903 (+)NCBIMhudiblu_PPA_v0panPan3
ACACA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1936,904,204 - 37,188,096 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl936,905,293 - 37,187,892 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha936,128,994 - 36,412,715 (-)NCBI
ROS_Cfam_1.0937,714,414 - 37,998,482 (-)NCBI
UMICH_Zoey_3.1936,495,840 - 36,779,686 (-)NCBI
UNSW_CanFamBas_1.0936,783,386 - 37,067,528 (-)NCBI
UU_Cfam_GSD_1.0936,870,310 - 37,154,200 (-)NCBI
Acaca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560235,883,567 - 36,147,281 (-)NCBI
SpeTri2.0NW_004936490927,769 - 1,191,483 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ACACA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1238,581,449 - 38,875,134 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11238,580,916 - 38,875,067 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21240,200,228 - 40,401,426 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ACACA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11630,374,166 - 30,704,635 (+)NCBI
ChlSab1.1 Ensembl1630,452,343 - 30,705,004 (+)Ensembl
Vero_WHO_p1.0NW_0236660771,098,931 - 1,432,102 (+)NCBI
Acaca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248714,103,014 - 4,364,690 (-)NCBI

Position Markers
D17S1255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21069,130,306 - 69,130,416 (+)MAPPERmRatBN7.2
Rnor_6.01071,575,744 - 71,575,853NCBIRnor6.0
Rnor_5.01071,485,875 - 71,485,984UniSTSRnor5.0
RGSC_v3.41072,532,258 - 72,532,367UniSTSRGSC3.4
Celera1068,057,375 - 68,057,484UniSTS
Cytogenetic Map10q26UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106592723382565079Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
631565Hcuc4Hepatic copper content QTL 44.15hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)106694181373452992Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106750210873579767Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642290Bp299Blood pressure QTL 299arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106823013469282520Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:53
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000041140
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 27 49 33 17 33 3 3 74 28 41 11 3
Low 2 16 8 8 2 8 5 8 7 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039086758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC096263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF121986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF121987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB871887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB873147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB875018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB879528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB888263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB921072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC929296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC930556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC932427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC936937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC945672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC978481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J03808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M31459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M31460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M31461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X53003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041140   ⟹   ENSRNOP00000049438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,066,860 - 69,276,457 (+)Ensembl
Rnor_6.0 Ensembl1071,546,977 - 71,719,910 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088138   ⟹   ENSRNOP00000073421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,099,659 - 69,276,457 (+)Ensembl
Rnor_6.0 Ensembl1071,536,533 - 71,719,910 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101496   ⟹   ENSRNOP00000078963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,066,860 - 69,276,457 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115196   ⟹   ENSRNOP00000094595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,066,860 - 69,276,457 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116202   ⟹   ENSRNOP00000086394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,014,170 - 69,276,457 (+)Ensembl
RefSeq Acc Id: NM_022193   ⟹   NP_071529
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,082,822 - 69,274,487 (+)NCBI
Rnor_6.01071,519,392 - 71,719,910 (+)NCBI
Rnor_5.01071,431,885 - 71,630,271 (+)NCBI
RGSC_v3.41072,483,772 - 72,677,134 (+)RGD
Celera1068,011,070 - 68,201,435 (+)RGD
Sequence:
RefSeq Acc Id: XM_039086752   ⟹   XP_038942680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,014,261 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086753   ⟹   XP_038942681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,014,261 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086754   ⟹   XP_038942682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,066,698 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086755   ⟹   XP_038942683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,066,698 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086756   ⟹   XP_038942684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,067,447 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086757   ⟹   XP_038942685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,066,698 - 69,276,453 (+)NCBI
RefSeq Acc Id: XM_039086758   ⟹   XP_038942686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,014,504 - 69,276,453 (+)NCBI
Protein Sequences
Protein RefSeqs NP_071529 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942680 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942681 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942682 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942683 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942684 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942685 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942686 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40652 (Get FASTA)   NCBI Sequence Viewer  
  AAA40653 (Get FASTA)   NCBI Sequence Viewer  
  AAA40654 (Get FASTA)   NCBI Sequence Viewer  
  AAA40655 (Get FASTA)   NCBI Sequence Viewer  
  AAA40656 (Get FASTA)   NCBI Sequence Viewer  
  ABL63425 (Get FASTA)   NCBI Sequence Viewer  
  ABL63426 (Get FASTA)   NCBI Sequence Viewer  
  CBF60000 (Get FASTA)   NCBI Sequence Viewer  
  CBF60635 (Get FASTA)   NCBI Sequence Viewer  
  CBF61881 (Get FASTA)   NCBI Sequence Viewer  
  CBF64062 (Get FASTA)   NCBI Sequence Viewer  
  CBF68276 (Get FASTA)   NCBI Sequence Viewer  
  CBF95526 (Get FASTA)   NCBI Sequence Viewer  
  CBU85244 (Get FASTA)   NCBI Sequence Viewer  
  CBU85853 (Get FASTA)   NCBI Sequence Viewer  
  CBU86757 (Get FASTA)   NCBI Sequence Viewer  
  CBU88938 (Get FASTA)   NCBI Sequence Viewer  
  CBU93150 (Get FASTA)   NCBI Sequence Viewer  
  CBV09046 (Get FASTA)   NCBI Sequence Viewer  
  EDM05508 (Get FASTA)   NCBI Sequence Viewer  
  EDM05509 (Get FASTA)   NCBI Sequence Viewer  
  EDM05510 (Get FASTA)   NCBI Sequence Viewer  
  EDM05511 (Get FASTA)   NCBI Sequence Viewer  
  P11497 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071529   ⟸   NM_022193
- UniProtKB: P11497 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000049438   ⟸   ENSRNOT00000041140
RefSeq Acc Id: ENSRNOP00000073421   ⟸   ENSRNOT00000088138
RefSeq Acc Id: XP_038942680   ⟸   XM_039086752
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038942681   ⟸   XM_039086753
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038942686   ⟸   XM_039086758
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942683   ⟸   XM_039086755
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942682   ⟸   XM_039086754
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942685   ⟸   XM_039086757
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942684   ⟸   XM_039086756
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000094595   ⟸   ENSRNOT00000115196
RefSeq Acc Id: ENSRNOP00000086394   ⟸   ENSRNOT00000116202
RefSeq Acc Id: ENSRNOP00000078963   ⟸   ENSRNOT00000101496
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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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)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621248 AgrOrtholog
Ensembl Genes ENSRNOG00000034013 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000049438 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073421 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041140 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088138 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1490.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AcCoA_carboxyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AcCoA_COase_cen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP-grasp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP_grasp_subdomain_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BC-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_carboxylation_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_COase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CbamoylP_synth_lsu-like_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ClpP/crotonase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COA_CT_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COA_CT_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PreATP-grasp_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rudment_hybrid_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Single_hybrid_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60581 UniProtKB/Swiss-Prot
NCBI Gene 60581 ENTREZGENE
Pfam ACC_central UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_carb_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_carb_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carboxyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSase_L_D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Acaca PhenoGen
PROSITE ATP_GRASP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BIOTIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BIOTINYL_LIPOYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COA_CT_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COA_CT_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CPSASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50979 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Biotin_carb_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51230 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51246 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52096 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5G8_RAT UniProtKB/TrEMBL
  ACACA_RAT UniProtKB/Swiss-Prot
  D3ZRA3_RAT UniProtKB/TrEMBL
  P11497 ENTREZGENE
UniProt Secondary A1EC79 UniProtKB/Swiss-Prot
  P97902 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-28 Acaca  acetyl-CoA carboxylase alpha  Acaca  acetyl-coenzyme A carboxylase alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Acaca  acetyl-coenzyme A carboxylase alpha  Acac  acetyl-coenzyme A carboxylase  Symbol and Name updated 1299863 APPROVED
2002-08-07 Acac  acetyl-coenzyme A carboxylase      Symbol and Name status set to provisional 70820 PROVISIONAL