Gabrb1 (gamma-aminobutyric acid type A receptor subunit beta1) - Rat Genome Database

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Gene: Gabrb1 (gamma-aminobutyric acid type A receptor subunit beta1) Rattus norvegicus
Analyze
Symbol: Gabrb1
Name: gamma-aminobutyric acid type A receptor subunit beta1
RGD ID: 2649
Description: Enables GABA receptor binding activity; GABA-A receptor activity; and ion channel activity. Involved in several processes, including cellular response to histamine; central nervous system neuron development; and response to progesterone. Located in several cellular components, including GABA-ergic synapse; dendrite; and nuclear envelope. Is integral component of plasma membrane. Part of GABA-A receptor complex. Biomarker of hepatic encephalopathy. Human ortholog(s) of this gene implicated in autistic disorder and developmental and epileptic encephalopathy 45. Orthologous to human GABRB1 (gamma-aminobutyric acid type A receptor subunit beta1); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GABA(A) receptor subunit beta-1; gamma-aminobutyric acid (GABA) A receptor, beta 1; gamma-aminobutyric acid (GABA-A) receptor, subunit beta 1; Gamma-aminobutyric acid receptor beta 1; gamma-aminobutyric acid receptor subunit beta-1; gamma-aminobutyric acid receptor, subunit beta 1; gamma-aminobutyric acid type A receptor beta 1 subunit; GARB1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Gabrb1Tn(pb-Bhr2)1Wmukf  
Is Marker For: Strains:   SD   WKY-Tg(Gabrb1Tn(pb-Bhr2)1Wmukf)  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21436,068,725 - 36,548,946 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1436,080,393 - 36,548,948 (-)Ensembl
Rnor_6.01438,631,192 - 39,112,598 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,643,385 - 39,112,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,453,142 - 38,924,073 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,530,259 - 39,005,615 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11438,532,649 - 39,008,000 (-)NCBI
Celera1435,310,585 - 35,771,142 (-)NCBICelera
Cytogenetic Map14p11NCBI
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
1,1,1-trichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2,2-trifluoroethanol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3alpha-hydroxy-5beta-pregnan-20-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bicuculline  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylparaben  (EXP)
chloral hydrate  (ISO)
Chloralose  (ISO)
chlorobutanol  (ISO)
cocaine  (EXP)
DDE  (EXP)
delta-hexachlorocyclohexane  (ISO)
dexamethasone  (EXP)
diazepam  (EXP,ISO)
dibutyl phthalate  (EXP)
dorsomorphin  (ISO)
endosulfan  (ISO)
enflurane  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
ether  (ISO)
etomidate  (ISO)
felbamate  (ISO)
fipronil  (ISO)
flumazenil  (EXP)
flurotyl  (EXP)
folic acid  (ISO)
gamma-aminobutyric acid  (EXP,ISO)
gamma-hexachlorocyclohexane  (ISO)
genistein  (ISO)
isoflurane  (ISO)
kainic acid  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linuron  (EXP)
methoxyflurane  (ISO)
muscimol  (EXP)
N,N-diethyl-m-toluamide  (EXP)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
pentobarbital  (EXP,ISO)
permethrin  (EXP)
picrotoxin  (ISO)
picrotoxinin  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (EXP)
propofol  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
sevoflurane  (ISO)
sodium arsenite  (ISO)
tert-butanol  (ISO)
tetrachloromethane  (EXP)
toluene  (ISO)
tribromoethanol  (ISO)
trichloroethene  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
zaleplon  (EXP)
zolpidem  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Brandon NJ, etal., J Neurosci 2002 Aug 1;22(15):6353-61.
2. Cai X, etal., J Physiol 2002 May 1;540(Pt 3):743-59.
3. Collins AL, etal., Neurogenetics. 2006 Jul;7(3):167-74. Epub 2006 Jun 13.
4. Fatemi SH, etal., J Autism Dev Disord. 2010 Jun;40(6):743-50.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Griffiths J and Lovick T, J Comp Neurol. 2005 May 23;486(1):89-97.
8. Griffiths JL and Lovick TA, Neuroscience. 2005;136(2):457-66. Epub 2005 Oct 13.
9. Huntsman MM and Huguenard JR, J Physiol. 2006 Apr 15;572(Pt 2):459-75. doi: 10.1113/jphysiol.2006.106617. Epub 2006 Feb 9.
10. Li S, etal., Brain Res Dev Brain Res. 2004 Jun 21;150(2):141-50.
11. Li XQ, etal., World J Gastroenterol. 2005 Jun 7;11(21):3319-22.
12. Lolait SJ, etal., FEBS Lett. 1989 Mar 27;246(1-2):145-8.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Sarang SS, etal., J Pharmacol Exp Ther. 2008 Jan;324(1):376-82. Epub 2007 Oct 24.
19. Saras A, etal., J Biol Chem. 2008 Apr 18;283(16):10470-5. doi: 10.1074/jbc.M709993200. Epub 2008 Feb 15.
20. Sergeeva OA, etal., J Biol Chem. 2010 Jul 30;285(31):23985-93. Epub 2010 May 28.
21. Shan Q, etal., J Biol Chem 2002 Nov 22;277(47):44845-53.
22. Sigel E, etal., FEBS Lett. 1989 Nov 6;257(2):377-9.
23. Ymer S, etal., EMBO J 1989 Jun;8(6):1665-70.
Additional References at PubMed
PMID:1977069   PMID:9039914   PMID:15014066   PMID:15708482   PMID:18338268   PMID:21242699   PMID:21735059   PMID:22215379   PMID:23176253   PMID:26950270   PMID:29706582   PMID:33636639  


Genomics

Comparative Map Data
Gabrb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21436,068,725 - 36,548,946 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1436,080,393 - 36,548,948 (-)Ensembl
Rnor_6.01438,631,192 - 39,112,598 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,643,385 - 39,112,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,453,142 - 38,924,073 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,530,259 - 39,005,615 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11438,532,649 - 39,008,000 (-)NCBI
Celera1435,310,585 - 35,771,142 (-)NCBICelera
Cytogenetic Map14p11NCBI
GABRB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl446,993,723 - 47,426,447 (+)EnsemblGRCh38hg38GRCh38
GRCh38446,993,560 - 47,438,409 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37447,033,584 - 47,428,464 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36446,728,336 - 47,123,202 (+)NCBINCBI36hg18NCBI36
Build 34446,874,506 - 47,269,373NCBI
Celera447,482,542 - 47,877,035 (+)NCBI
Cytogenetic Map4p12NCBI
HuRef446,352,751 - 46,747,922 (+)NCBIHuRef
CHM1_1447,032,490 - 47,427,496 (+)NCBICHM1_1
Gabrb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39571,815,264 - 72,306,915 (+)NCBIGRCm39mm39
GRCm39 Ensembl571,815,456 - 72,306,380 (+)Ensembl
GRCm38571,657,921 - 72,149,572 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl571,658,113 - 72,149,037 (+)EnsemblGRCm38mm10GRCm38
MGSCv37572,091,255 - 72,528,483 (+)NCBIGRCm37mm9NCBIm37
MGSCv36571,979,151 - 72,416,379 (+)NCBImm8
Celera568,964,933 - 69,390,319 (+)NCBICelera
Cytogenetic Map5C3.2NCBI
cM Map538.18NCBI
Gabrb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554431,132,860 - 1,514,376 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554431,126,223 - 1,514,291 (-)NCBIChiLan1.0ChiLan1.0
GABRB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1485,458,810 - 85,894,427 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl485,459,225 - 85,857,321 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0474,727,321 - 75,164,407 (-)NCBIMhudiblu_PPA_v0panPan3
GABRB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11343,011,491 - 43,349,876 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1342,992,569 - 43,349,923 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1342,942,633 - 43,300,315 (+)NCBI
ROS_Cfam_1.01343,598,384 - 43,955,432 (+)NCBI
UMICH_Zoey_3.11343,276,378 - 43,634,632 (+)NCBI
UU_Cfam_GSD_1.01343,691,479 - 44,049,754 (+)NCBI
Gabrb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528532,699,565 - 33,078,224 (-)NCBI
SpeTri2.0NW_00493648213,219,962 - 13,593,868 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GABRB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl836,978,547 - 37,355,009 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1836,978,014 - 37,354,950 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2839,176,670 - 39,275,449 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GABRB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1272,829,385 - 3,254,292 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl272,832,450 - 3,217,326 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604748,873,122 - 49,316,579 (-)NCBIVero_WHO_p1.0
Gabrb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476119,595,802 - 20,019,368 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Hmgc7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21436,269,082 - 36,269,300 (+)MAPPERmRatBN7.2
Rnor_6.01438,832,884 - 38,833,099NCBIRnor6.0
Rnor_5.01438,642,398 - 38,642,613UniSTSRnor5.0
RGSC_v3.41438,725,068 - 38,725,284RGDRGSC3.4
RGSC_v3.41438,725,069 - 38,725,284UniSTSRGSC3.4
Celera1435,501,589 - 35,501,804UniSTS
Cytogenetic Map14p11UniSTS
U14418  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21436,080,606 - 36,080,713 (+)MAPPERmRatBN7.2
Rnor_6.01438,643,599 - 38,643,705NCBIRnor6.0
Rnor_5.01438,453,370 - 38,453,476UniSTSRnor5.0
RGSC_v3.41438,530,487 - 38,530,593UniSTSRGSC3.4
Celera1435,310,813 - 35,310,919UniSTS
Cytogenetic Map14p11UniSTS
RH94648  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21436,080,412 - 36,080,565 (+)MAPPERmRatBN7.2
Rnor_6.01438,643,405 - 38,643,557NCBIRnor6.0
Rnor_5.01438,453,176 - 38,453,328UniSTSRnor5.0
RGSC_v3.41438,530,293 - 38,530,445UniSTSRGSC3.4
Celera1435,310,619 - 35,310,771UniSTS
Cytogenetic Map14p11UniSTS
Gabrb1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21436,080,435 - 36,081,128 (+)MAPPERmRatBN7.2
Rnor_6.01438,643,428 - 38,644,120NCBIRnor6.0
Rnor_5.01438,453,199 - 38,453,891UniSTSRnor5.0
RGSC_v3.41438,530,316 - 38,531,008UniSTSRGSC3.4
Celera1435,310,642 - 35,311,334UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat


Related Rat Strains
The following Strains have been annotated to Gabrb1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:55
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000003170
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

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 23
Low 1 1 41 6
Below cutoff 25 9 4 5 4 6 7 8 17 22 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003170   ⟹   ENSRNOP00000003170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1436,080,393 - 36,548,948 (-)Ensembl
Rnor_6.0 Ensembl1438,643,385 - 39,112,600 (-)Ensembl
RefSeq Acc Id: NM_012956   ⟹   NP_037088
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21436,080,380 - 36,548,946 (-)NCBI
Rnor_6.01438,643,371 - 39,112,598 (-)NCBI
Rnor_5.01438,453,142 - 38,924,073 (-)NCBI
RGSC_v3.41438,530,259 - 39,005,615 (-)RGD
Celera1435,310,585 - 35,771,142 (-)RGD
Sequence:
RefSeq Acc Id: XM_039091637   ⟹   XP_038947565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21436,068,725 - 36,112,734 (-)NCBI
Protein Sequences
Protein RefSeqs NP_037088 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947565 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA33493 (Get FASTA)   NCBI Sequence Viewer  
  EDL90004 (Get FASTA)   NCBI Sequence Viewer  
  P15431 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037088   ⟸   NM_012956
- Peptide Label: precursor
- UniProtKB: P15431 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003170   ⟸   ENSRNOT00000003170
RefSeq Acc Id: XP_038947565   ⟸   XM_039091637
- Peptide Label: isoform X1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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)
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
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/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
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)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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/RijCrl (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: 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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2649 AgrOrtholog
Ensembl Genes ENSRNOG00000002327 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003170 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003170 UniProtKB/Swiss-Prot
Gene3D-CATH 2.70.170.10 UniProtKB/Swiss-Prot
InterPro GABAA/Glycine_rcpt UniProtKB/Swiss-Prot
  GABAAb_rcpt UniProtKB/Swiss-Prot
  Neur_chan_lig-bd UniProtKB/Swiss-Prot
  Neur_chan_lig-bd_sf UniProtKB/Swiss-Prot
  Neur_channel UniProtKB/Swiss-Prot
  Neuro-gated_channel_TM_sf UniProtKB/Swiss-Prot
  Neurotrans-gated_channel_TM UniProtKB/Swiss-Prot
  Neurotransmitter_ion_chnl_CS UniProtKB/Swiss-Prot
KEGG Report rno:25450 UniProtKB/Swiss-Prot
NCBI Gene 25450 ENTREZGENE
PANTHER PTHR18945 UniProtKB/Swiss-Prot
Pfam Neur_chan_LBD UniProtKB/Swiss-Prot
  Neur_chan_memb UniProtKB/Swiss-Prot
PhenoGen Gabrb1 PhenoGen
PRINTS GABAARBETA UniProtKB/Swiss-Prot
  GABAARECEPTR UniProtKB/Swiss-Prot
  NRIONCHANNEL UniProtKB/Swiss-Prot
PROSITE NEUROTR_ION_CHANNEL UniProtKB/Swiss-Prot
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot
  SSF90112 UniProtKB/Swiss-Prot
TIGRFAMs LIC UniProtKB/Swiss-Prot
UniProt GBRB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Gabrb1  gamma-aminobutyric acid type A receptor beta 1 subunit  Gabrb1  gamma-aminobutyric acid (GABA) A receptor, beta 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-04 Gabrb1  gamma-aminobutyric acid (GABA) A receptor, beta 1  Gabrb1  gamma-aminobutyric acid (GABA-A) receptor, subunit beta 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Gabrb1  gamma-aminobutyric acid (GABA-A) receptor, subunit beta 1    gamma-aminobutyric acid receptor, subunit beta 1  Name updated 1299863 APPROVED
2002-11-06 Gabrb1  gamma-aminobutyric acid receptor, subunit beta 1    Gamma-aminobutyric acid receptor beta 1  Name updated 625702 APPROVED
2002-06-10 Gabrb1  Gamma-aminobutyric acid receptor beta 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in neuron cells of brain 625749
gene_process mediates in inhibitory neurotransmission in the brain 625749
gene_protein 58 kDa 625749
gene_regulation activated by C kinase (RACK-1) and protein kinase C (PKC) 625749
gene_regulation modulation of function occurs by the phosphorylation of residues within the intracellular domains of the receptor subunits by serine/threonine and tyrosine kinases 625749
gene_regulation RACK-1 increases GABA(A) receptor function in neurons by a PKC-dependent signaling pathway by way of activating the muscarinic acetylcholine receptors (mAChRs) 625749