Acacb (acetyl-CoA carboxylase beta) - Rat Genome Database

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Gene: Acacb (acetyl-CoA carboxylase beta) Rattus norvegicus
Analyze
Symbol: Acacb
Name: acetyl-CoA carboxylase beta
RGD ID: 620500
Description: Enables biotin binding activity. Involved in response to organic cyclic compound and response to xenobiotic stimulus. Located in mitochondrion. Used to study fatty liver disease. Orthologous to human ACACB (acetyl-CoA carboxylase beta); PARTICIPATES IN fatty acid biosynthetic pathway; insulin signaling pathway; propanoate metabolic pathway; INTERACTS WITH (+)-catechin; (+)-schisandrin B; (R)-mevalonic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Acc2; acetyl-CoA carboxylase 2; acetyl-Coenzyme A carboxylase 2; acetyl-Coenzyme A carboxylase beta
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
mRatBN7.21242,365,800 - 42,477,651 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.01248,127,149 - 48,238,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,127,149 - 48,238,887 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01249,914,427 - 50,000,957 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41243,388,679 - 43,492,993 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11243,252,066 - 43,356,381 (-)NCBI
Celera1243,976,897 - 44,062,163 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP)
(+)-schisandrin B  (EXP)
(R)-mevalonic acid  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
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  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
aspartame  (ISO)
atorvastatin calcium  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cyanocob(III)alamin  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
D-mannitol  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
fenofibrate  (ISO)
folic acid  (ISO)
fructose  (EXP,ISO)
furan  (ISO)
genistein  (ISO)
glucose  (ISO)
glycine betaine  (ISO)
GW 4064  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
metformin  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
monosodium L-glutamate  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
O-methyleugenol  (ISO)
olaparib  (ISO)
oleic acid  (ISO)
ozone  (EXP)
paracetamol  (EXP,ISO)
paraquat  (EXP)
PCB138  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
puerarin  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tenofovir disoproxil fumarate  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zidovudine  (ISO)
zinc atom  (EXP,ISO)
zinc sulfate  (EXP)
zinc(0)  (EXP,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11283375   PMID:12764144   PMID:12920182   PMID:15579580   PMID:15590647   PMID:15677334   PMID:16854592   PMID:17210641   PMID:17956983   PMID:18255222   PMID:18487439   PMID:18614015  
PMID:19236960   PMID:19618481   PMID:20457939   PMID:20952656   PMID:25195817   PMID:26976583  


Genomics

Candidate Gene Status
Acacb is a candidate Gene for QTL Bw128
Acacb is a candidate Gene for QTL Bw132
Acacb is a candidate Gene for QTL Foco6
Acacb is a candidate Gene for QTL Foco10
Acacb is a candidate Gene for QTL Foco20
Comparative Map Data
Acacb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21242,365,800 - 42,477,651 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.01248,127,149 - 48,238,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,127,149 - 48,238,887 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01249,914,427 - 50,000,957 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41243,388,679 - 43,492,993 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11243,252,066 - 43,356,381 (-)NCBI
Celera1243,976,897 - 44,062,163 (-)NCBICelera
Cytogenetic Map12q16NCBI
ACACB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12109,116,587 - 109,268,226 (+)EnsemblGRCh38hg38GRCh38
GRCh3812109,112,666 - 109,268,226 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712109,554,392 - 109,706,031 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612108,061,585 - 108,190,414 (+)NCBINCBI36hg18NCBI36
Build 3412108,039,930 - 108,166,887NCBI
Celera12109,201,352 - 109,330,479 (+)NCBI
Cytogenetic Map12q24.11NCBI
HuRef12106,595,722 - 106,724,234 (+)NCBIHuRef
CHM1_112109,544,852 - 109,673,937 (+)NCBICHM1_1
Acacb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395114,284,378 - 114,388,822 (+)NCBIGRCm39mm39
GRCm39 Ensembl5114,284,596 - 114,388,822 (+)Ensembl
GRCm385114,146,321 - 114,250,761 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5114,146,535 - 114,250,761 (+)EnsemblGRCm38mm10GRCm38
MGSCv375114,615,527 - 114,700,767 (+)NCBIGRCm37mm9NCBIm37
MGSCv365114,426,517 - 114,510,733 (+)NCBImm8
Celera5111,267,324 - 111,357,484 (+)NCBICelera
Cytogenetic Map5FNCBI
Acacb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545510,308,192 - 10,426,076 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545510,282,308 - 10,427,439 (+)NCBIChiLan1.0ChiLan1.0
ACACB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112110,086,374 - 110,239,847 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12110,086,374 - 110,239,847 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012106,692,668 - 106,845,490 (+)NCBIMhudiblu_PPA_v0panPan3
ACACB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12617,763,531 - 17,895,319 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2617,747,362 - 17,894,400 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2617,906,250 - 18,037,960 (+)NCBI
ROS_Cfam_1.02618,106,936 - 18,239,349 (-)NCBI
ROS_Cfam_1.0 Ensembl2618,106,944 - 18,239,179 (-)Ensembl
UMICH_Zoey_3.12618,115,480 - 18,247,107 (+)NCBI
UNSW_CanFamBas_1.02618,097,758 - 18,229,980 (-)NCBI
UU_Cfam_GSD_1.02618,116,847 - 18,248,772 (-)NCBI
Acacb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118144,422,223 - 144,525,063 (-)NCBI
SpeTri2.0NW_004936769950,970 - 1,053,671 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ACACB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11441,621,574 - 41,739,916 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21444,153,373 - 44,271,216 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ACACB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111104,325,250 - 104,488,567 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11104,349,573 - 104,488,003 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037140,614,337 - 140,773,620 (-)NCBIVero_WHO_p1.0
Acacb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474712,287,817 - 12,426,340 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:86
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000000821, ENSRNOT00000067975
Prediction methods:Microtar, Miranda, Rnahybrid
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 43 22 13 3 13 8 11 21 5 11 8
Low 3 35 28 16 28 72 14 36
Below cutoff 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB004329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC131519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AM237460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ493871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB872073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB873333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB875204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB879714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB888449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HB921258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC929482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC930742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC932613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC937123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC945858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HC978667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000821   ⟹   ENSRNOP00000000821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.0 Ensembl1248,128,408 - 48,218,955 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067975   ⟹   ENSRNOP00000060736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.0 Ensembl1248,128,405 - 48,218,955 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078868   ⟹   ENSRNOP00000071816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.0 Ensembl1248,127,149 - 48,238,887 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080557   ⟹   ENSRNOP00000073473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,366,548 - 42,457,655 (-)Ensembl
Rnor_6.0 Ensembl1248,128,405 - 48,218,955 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113138   ⟹   ENSRNOP00000094530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,366,548 - 42,448,848 (-)Ensembl
RefSeq Acc Id: NM_053922   ⟹   NP_446374
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,477,651 (-)NCBI
Rnor_6.01248,128,405 - 48,218,955 (-)NCBI
Rnor_5.01249,914,427 - 50,000,957 (-)NCBI
RGSC_v3.41243,388,679 - 43,492,993 (-)RGD
Celera1243,976,897 - 44,062,163 (-)RGD
Sequence:
RefSeq Acc Id: XM_017598242   ⟹   XP_017453731
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,477,509 (-)NCBI
Rnor_6.01248,127,149 - 48,238,969 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598243   ⟹   XP_017453732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,467,804 (-)NCBI
Rnor_6.01248,127,149 - 48,229,431 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598245   ⟹   XP_017453734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,466,946 (-)NCBI
Rnor_6.01248,127,149 - 48,228,340 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598246   ⟹   XP_017453735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,477,508 (-)NCBI
Rnor_6.01248,127,149 - 48,238,969 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598247   ⟹   XP_017453736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,448,872 (-)NCBI
Rnor_6.01248,127,149 - 48,210,393 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598248   ⟹   XP_017453737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,442,942 (-)NCBI
Rnor_6.01248,127,149 - 48,205,056 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089030   ⟹   XP_038944958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,365,800 - 42,457,635 (-)NCBI
RefSeq Acc Id: XM_039089031   ⟹   XP_038944959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,391,852 - 42,477,587 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446374   ⟸   NM_053922
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_017453735   ⟸   XM_017598246
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453731   ⟸   XM_017598242
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453732   ⟸   XM_017598243
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453734   ⟸   XM_017598245
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453736   ⟸   XM_017598247
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017453737   ⟸   XM_017598248
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000073473   ⟸   ENSRNOT00000080557
RefSeq Acc Id: ENSRNOP00000060736   ⟸   ENSRNOT00000067975
RefSeq Acc Id: ENSRNOP00000000821   ⟸   ENSRNOT00000000821
RefSeq Acc Id: ENSRNOP00000071816   ⟸   ENSRNOT00000078868
RefSeq Acc Id: XP_038944958   ⟸   XM_039089030
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944959   ⟸   XM_039089031
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000094530   ⟸   ENSRNOT00000113138
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)
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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
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)
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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
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 48218640 48218641 T G snv BBDP/Wor (RGD), LEW/Crl (2019), LEW/NCrlBR (RGD), LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620500 AgrOrtholog
Ensembl Genes ENSRNOG00000000658 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000821 UniProtKB/TrEMBL
  ENSRNOP00000060736 UniProtKB/TrEMBL
  ENSRNOP00000071816 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073473 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000094530 ENTREZGENE
Ensembl Transcript ENSRNOT00000000821 UniProtKB/TrEMBL
  ENSRNOT00000067975 UniProtKB/TrEMBL
  ENSRNOT00000078868 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080557 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000113138 ENTREZGENE
Gene3D-CATH 3.30.1490.20 UniProtKB/TrEMBL
InterPro AcCoA_carboxyl UniProtKB/TrEMBL
  AcCoA_COase_cen UniProtKB/TrEMBL
  ATP-grasp UniProtKB/TrEMBL
  ATP_grasp_subdomain_1 UniProtKB/TrEMBL
  Biotin_carboxylation_dom UniProtKB/TrEMBL
  Biotin_COase_C UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_ATP-bd UniProtKB/TrEMBL
  CarbamoylP_synth_lsu_N UniProtKB/TrEMBL
  ClpP/crotonase-like_dom UniProtKB/TrEMBL
  COA_CT_C UniProtKB/TrEMBL
  COA_CT_N UniProtKB/TrEMBL
  PreATP-grasp-like UniProtKB/TrEMBL
  Rudment_hybrid_motif UniProtKB/TrEMBL
  Single_hybrid_motif UniProtKB/TrEMBL
KEGG Report rno:116719 UniProtKB/TrEMBL
NCBI Gene 116719 ENTREZGENE
Pfam ACC_central UniProtKB/TrEMBL
  Biotin_carb_C UniProtKB/TrEMBL
  Biotin_lipoyl UniProtKB/TrEMBL
  Carboxyl_trans UniProtKB/TrEMBL
  CPSase_L_chain UniProtKB/TrEMBL
  CPSase_L_D2 UniProtKB/TrEMBL
PhenoGen Acacb PhenoGen
PROSITE ATP_GRASP UniProtKB/TrEMBL
  BIOTINYL_LIPOYL UniProtKB/TrEMBL
  COA_CT_CTER UniProtKB/TrEMBL
  COA_CT_NTER UniProtKB/TrEMBL
  CPSASE_1 UniProtKB/TrEMBL
  CPSASE_2 UniProtKB/TrEMBL
  PS50979 UniProtKB/TrEMBL
SMART Biotin_carb_C UniProtKB/TrEMBL
Superfamily-SCOP Hybrid_motif UniProtKB/TrEMBL
  PreATP-grasp-like UniProtKB/TrEMBL
  Rudmnt_hyb_motif UniProtKB/TrEMBL
  SSF52096 UniProtKB/TrEMBL
UniProt A0A0G2K1F2_RAT UniProtKB/TrEMBL
  A0A0G2K5L6_RAT UniProtKB/TrEMBL
  B7ZDJ4_RAT UniProtKB/TrEMBL
  D3ZBE2_RAT UniProtKB/TrEMBL
  E9PSQ0_RAT UniProtKB/TrEMBL
  O70151_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-28 Acacb  acetyl-CoA carboxylase beta  Acacb  acetyl-Coenzyme A carboxylase beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Acacb  acetyl-Coenzyme A carboxylase beta      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Acacb  acetyl-Coenzyme A carboxylase beta      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed at high levels in heart, skeletal muscle, and brown adipose tissue 631890
gene_regulation synergystically regulated by sterol regulatory element-binding protein-1 (SREBP1). 631890