Bcat1 (branched chain amino acid transaminase 1) - Rat Genome Database

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Gene: Bcat1 (branched chain amino acid transaminase 1) Rattus norvegicus
Analyze
Symbol: Bcat1
Name: branched chain amino acid transaminase 1
RGD ID: 2195
Description: Enables branched-chain-amino-acid transaminase activity and identical protein binding activity. Predicted to be involved in leucine biosynthetic process and valine biosynthetic process. Predicted to act upstream of or within branched-chain amino acid catabolic process. Located in cytoplasm. Orthologous to human BCAT1 (branched chain amino acid transaminase 1); PARTICIPATES IN 3-hydroxy-3-methylglutaryl-CoA lyase deficiency pathway; 3-hydroxyisobutyric aciduria pathway; 3-methylcrotonyl CoA carboxylase 1 deficiency pathway; INTERACTS WITH 17alpha-ethynylestradiol; 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BCAT(c); Bcatc; branched chain amino acid transaminase 1, cytosolic; branched chain aminotransferase 1, cytosolic; branched-chain-amino-acid aminotransferase, cytosolic; MGC105472
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Bcat1em2Mcwi  
Genetic Models: SS-Bcat1em2Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24177,964,834 - 178,046,573 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4177,964,834 - 178,046,597 (-)Ensembl
Rnor_6.04179,259,305 - 179,340,021 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4179,259,308 - 179,339,795 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04243,463,299 - 243,491,574 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.04243,444,839 - 243,460,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44182,641,517 - 182,692,917 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14182,886,640 - 182,938,041 (-)NCBI
Celera4166,483,269 - 166,533,125 (-)NCBICelera
Cytogenetic Map4q44NCBI
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
(-)-demecolcine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
allyl alcohol  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bucladesine  (ISO)
Butylbenzyl phthalate  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcidiol  (EXP)
carbamazepine  (ISO)
carbofuran  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
cisplatin  (EXP,ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (EXP,ISO)
DDT  (EXP)
deguelin  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (EXP)
diethyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
heptachlor  (EXP)
ifosfamide  (ISO)
isoprenaline  (EXP)
lead diacetate  (EXP,ISO)
medroxyprogesterone acetate  (ISO)
metacetamol  (ISO)
metaproterenol  (EXP)
methapyrilene  (EXP,ISO)
methyl methanesulfonate  (ISO)
mirex  (EXP)
mitoxantrone  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
neomycin  (ISO)
nickel atom  (ISO)
orciprenaline  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
pentane-2,3-dione  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
phenylbutazone  (EXP)
potassium chromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
scopolamine  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (EXP,ISO)
triamterene  (EXP)
tributylstannane  (EXP)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
cytosol  (ISO)
mitochondrion  (IBA)

References

Additional References at PubMed
PMID:12477932   PMID:14755340   PMID:15489334   PMID:16141215   PMID:17348860   PMID:18614015   PMID:22871113  


Genomics

Comparative Map Data
Bcat1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24177,964,834 - 178,046,573 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4177,964,834 - 178,046,597 (-)Ensembl
Rnor_6.04179,259,305 - 179,340,021 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4179,259,308 - 179,339,795 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04243,463,299 - 243,491,574 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.04243,444,839 - 243,460,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44182,641,517 - 182,692,917 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14182,886,640 - 182,938,041 (-)NCBI
Celera4166,483,269 - 166,533,125 (-)NCBICelera
Cytogenetic Map4q44NCBI
BCAT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1224,810,024 - 24,949,101 (-)EnsemblGRCh38hg38GRCh38
GRCh381224,810,024 - 24,949,101 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371224,962,958 - 25,102,035 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361224,855,545 - 24,993,499 (-)NCBINCBI36hg18NCBI36
Build 341224,855,561 - 24,993,499NCBI
Celera1230,109,823 - 30,249,287 (-)NCBI
Cytogenetic Map12p12.1NCBI
HuRef1224,732,841 - 24,872,358 (-)NCBIHuRef
CHM1_11224,928,106 - 25,067,454 (-)NCBICHM1_1
Bcat1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396144,939,561 - 145,021,883 (-)NCBIGRCm39mm39
GRCm39 Ensembl6144,939,561 - 145,021,910 (-)Ensembl
GRCm386144,993,835 - 145,076,157 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6144,993,835 - 145,076,184 (-)EnsemblGRCm38mm10GRCm38
MGSCv376144,942,355 - 145,024,677 (-)NCBIGRCm37mm9NCBIm37
MGSCv366144,956,312 - 145,033,242 (-)NCBImm8
Celera6148,047,506 - 148,145,066 (-)NCBICelera
Cytogenetic Map6G3NCBI
cM Map677.27NCBI
Bcat1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541319,981,328 - 20,087,638 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541319,975,395 - 20,087,656 (-)NCBIChiLan1.0ChiLan1.0
BCAT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11263,978,116 - 64,114,127 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1263,978,116 - 64,107,463 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01261,364,154 - 61,500,827 (+)NCBIMhudiblu_PPA_v0panPan3
BCAT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12722,536,297 - 22,643,350 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2722,535,254 - 22,636,959 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2723,725,637 - 23,832,733 (-)NCBI
ROS_Cfam_1.02722,769,835 - 22,843,576 (+)NCBI
UMICH_Zoey_3.12722,584,192 - 22,657,415 (+)NCBI
UNSW_CanFamBas_1.02722,569,213 - 22,676,273 (+)NCBI
UU_Cfam_GSD_1.02723,897,853 - 24,005,177 (-)NCBI
Bcat1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494584,462,896 - 84,532,986 (+)NCBI
SpeTri2.0NW_0049365482,385,756 - 2,454,423 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCAT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl548,814,300 - 48,925,976 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1548,814,212 - 48,925,632 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2552,534,770 - 52,624,453 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BCAT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11124,578,760 - 24,709,541 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1124,579,487 - 24,709,132 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606910,417,680 - 10,554,451 (+)NCBIVero_WHO_p1.0
Bcat1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475214,074,701 - 14,166,075 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH137483  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24178,010,417 - 178,010,618 (+)MAPPERmRatBN7.2
Rnor_6.04179,304,131 - 179,304,331NCBIRnor6.0
Rnor_5.04243,488,610 - 243,488,810UniSTSRnor5.0
RGSC_v3.44182,689,953 - 182,690,153UniSTSRGSC3.4
Celera4166,530,161 - 166,530,361UniSTS
Cytogenetic Map4q44UniSTS
AU048984  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24177,986,839 - 177,987,023 (+)MAPPERmRatBN7.2
Rnor_6.04179,280,467 - 179,280,650NCBIRnor6.0
Rnor_5.04243,465,541 - 243,465,724UniSTSRnor5.0
RGSC_v3.44182,665,427 - 182,665,610UniSTSRGSC3.4
Celera4166,506,352 - 166,506,535UniSTS
Cytogenetic Map4q44UniSTS
RH128559  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24177,964,886 - 177,965,077 (+)MAPPERmRatBN7.2
Rnor_6.04179,259,358 - 179,259,548NCBIRnor6.0
Rnor_5.04243,444,892 - 243,445,082UniSTSRnor5.0
RGSC_v3.44182,641,570 - 182,641,760UniSTSRGSC3.4
Celera4166,483,322 - 166,483,512UniSTS
Cytogenetic Map4q44UniSTS
RH138612  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24178,011,088 - 178,011,232 (+)MAPPERmRatBN7.2
Rnor_6.04179,304,801 - 179,304,944NCBIRnor6.0
Rnor_5.04243,489,280 - 243,489,423UniSTSRnor5.0
RGSC_v3.44182,690,623 - 182,690,766UniSTSRGSC3.4
Celera4166,530,831 - 166,530,974UniSTS
RH 3.4 Map41077.3UniSTS
Cytogenetic Map4q44UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat


Genetic Models
This gene Bcat1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:90
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000021193
Prediction methods: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 7
Medium 2 22 18 6 9 6 67 14 30 3
Low 1 21 28 24 10 24 8 11 21 10 8 8
Below cutoff 11 11 11 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021193   ⟹   ENSRNOP00000021193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,834 - 178,012,316 (-)Ensembl
Rnor_6.0 Ensembl4179,259,310 - 179,307,095 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080410   ⟹   ENSRNOP00000074245
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,834 - 178,046,597 (-)Ensembl
Rnor_6.0 Ensembl4179,259,308 - 179,339,795 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097702   ⟹   ENSRNOP00000093677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,842 - 178,012,123 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117044   ⟹   ENSRNOP00000090195
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,834 - 178,046,411 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119115   ⟹   ENSRNOP00000085607
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,839 - 178,013,847 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000120070   ⟹   ENSRNOP00000082839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4177,964,836 - 178,013,245 (-)Ensembl
RefSeq Acc Id: NM_017253   ⟹   NP_058949
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,013,383 (-)NCBI
Rnor_6.04179,259,305 - 179,307,095 (-)NCBI
Rnor_5.04243,444,839 - 243,460,481 (-)NCBI
Rnor_5.04243,463,299 - 243,491,574 (-)NCBI
RGSC_v3.44182,641,517 - 182,692,917 (-)RGD
Celera4166,483,269 - 166,533,125 (-)RGD
Sequence:
RefSeq Acc Id: XM_008763370   ⟹   XP_008761592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,013,087 (-)NCBI
Rnor_6.04179,259,305 - 179,306,810 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763371   ⟹   XP_008761593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,046,518 (-)NCBI
Rnor_6.04179,259,305 - 179,340,021 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763372   ⟹   XP_008761594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,046,573 (-)NCBI
Rnor_6.04179,259,305 - 179,339,936 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763373   ⟹   XP_008761595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,012,429 (-)NCBI
Rnor_6.04179,259,305 - 179,306,141 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107212   ⟹   XP_038963140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24177,964,834 - 178,046,518 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058949   ⟸   NM_017253
- UniProtKB: P54690 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008761593   ⟸   XM_008763371
- Peptide Label: isoform X2
- UniProtKB: Q99JD5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761594   ⟸   XM_008763372
- Peptide Label: isoform X2
- UniProtKB: Q99JD5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761592   ⟸   XM_008763370
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761595   ⟸   XM_008763373
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000074245   ⟸   ENSRNOT00000080410
RefSeq Acc Id: ENSRNOP00000021193   ⟸   ENSRNOT00000021193
RefSeq Acc Id: XP_038963140   ⟸   XM_039107212
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000082839   ⟸   ENSRNOT00000120070
RefSeq Acc Id: ENSRNOP00000090195   ⟸   ENSRNOT00000117044
RefSeq Acc Id: ENSRNOP00000093677   ⟸   ENSRNOT00000097702
RefSeq Acc Id: ENSRNOP00000085607   ⟸   ENSRNOT00000119115

Transcriptome

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

Promoters
RGD ID:13693495
Promoter ID:EPDNEW_R4020
Type:initiation region
Name:Bcat1_2
Description:branched chain amino acid transaminase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4021  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04179,307,089 - 179,307,149EPDNEW
RGD ID:13693500
Promoter ID:EPDNEW_R4021
Type:initiation region
Name:Bcat1_1
Description:branched chain amino acid transaminase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R4020  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04179,339,774 - 179,339,834EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2195 AgrOrtholog
Ensembl Genes ENSRNOG00000015514 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021193 UniProtKB/Swiss-Prot
  ENSRNOP00000074245 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021193 UniProtKB/Swiss-Prot
  ENSRNOT00000080410 UniProtKB/TrEMBL
Gene3D-CATH 3.20.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.470.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7315507 IMAGE-MGC_LOAD
InterPro Aminotrans_IV UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Aminotrans_IV_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Aminotransferase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B_amino_transII UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BCAT-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BCAT-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BCAT_family UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29592 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105472 IMAGE-MGC_LOAD
NCBI Gene 29592 ENTREZGENE
Pfam Aminotran_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Bcat1 PhenoGen
PIRSF BCAT1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE AA_TRANSFER_CLASS_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56752 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs ilvE_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt BCAT1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q99JD5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-28 Bcat1  branched chain amino acid transaminase 1, cytosolic  Bcat1  branched chain aminotransferase 1, cytosolic  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Bcat1  branched chain aminotransferase 1, cytosolic      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the substantia nigra 631308
gene_function transferase 631308
gene_process may play a role in maintaining neuronal viability following striatal target injury 631308
gene_protein 46.0 kDa 69773
gene_regulation mRNA is upregulated in neurons following striatal target injury 631308