Gabra6 (gamma-aminobutyric acid type A receptor subunit alpha6) - Rat Genome Database

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Gene: Gabra6 (gamma-aminobutyric acid type A receptor subunit alpha6) Rattus norvegicus
Analyze
Symbol: Gabra6
Name: gamma-aminobutyric acid type A receptor subunit alpha6
RGD ID: 61861
Description: Exhibits inhibitory extracellular ligand-gated ion channel activity. Contributes to GABA-A receptor activity; GABA-gated chloride ion channel activity; and benzodiazepine receptor activity. Involved in GABAergic synaptic transmission. Localizes to several cellular components, including cerebellar Golgi cell to granule cell synapse; hippocampal mossy fiber to CA3 synapse; and synaptic membrane. Used to study obesity. Orthologous to human GABRA6 (gamma-aminobutyric acid type A receptor subunit alpha6); INTERACTS WITH (S)-nicotine; ammonium chloride; bicuculline.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GABA(A) receptor subunit alpha-6; GABA-A receptor alpha-6 subunit; gamma-aminobutyric acid (GABA) A receptor, alpha 6; gamma-aminobutyric acid (GABA-A) receptor subunit alpha 6; gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 6; gamma-aminobutyric acid A receptor, alpha 6; gamma-aminobutyric acid receptor subunit alpha-6; gamma-aminobutyric acid type A receptor alpha 6 subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   ANT  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21026,810,411 - 26,825,768 (-)NCBI
Rnor_6.0 Ensembl1027,847,439 - 27,862,868 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01027,847,447 - 27,862,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01027,691,630 - 27,706,971 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41027,474,071 - 27,489,074 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11027,475,119 - 27,490,123 (-)NCBI
Celera1026,323,497 - 26,337,672 (-)NCBICelera
Cytogenetic Map10q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:1312131   PMID:1312132   PMID:1346133   PMID:1379501   PMID:1665550   PMID:1966765   PMID:15579538   PMID:15950783   PMID:18056985   PMID:22521829   PMID:23602886   PMID:25128322  
PMID:26134650   PMID:27388150  


Genomics

Comparative Map Data
Gabra6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21026,810,411 - 26,825,768 (-)NCBI
Rnor_6.0 Ensembl1027,847,439 - 27,862,868 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01027,847,447 - 27,862,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01027,691,630 - 27,706,971 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41027,474,071 - 27,489,074 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11027,475,119 - 27,490,123 (-)NCBI
Celera1026,323,497 - 26,337,672 (-)NCBICelera
Cytogenetic Map10q21NCBI
GABRA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5161,547,063 - 161,702,593 (+)EnsemblGRCh38hg38GRCh38
GRCh385161,685,721 - 161,702,592 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375161,112,727 - 161,129,598 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365161,045,236 - 161,062,176 (+)NCBINCBI36hg18NCBI36
Build 345161,045,547 - 161,061,697NCBI
Celera5157,144,516 - 157,161,456 (+)NCBI
Cytogenetic Map5q34NCBI
HuRef5156,205,057 - 156,221,975 (+)NCBIHuRef
CHM1_15160,545,077 - 160,562,018 (+)NCBICHM1_1
Gabra6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391142,197,264 - 42,211,977 (-)NCBIGRCm39mm39
GRCm39 Ensembl1142,197,264 - 42,211,899 (-)Ensembl
GRCm381142,306,437 - 42,321,072 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1142,306,437 - 42,321,072 (-)EnsemblGRCm38mm10GRCm38
MGSCv371142,119,939 - 42,134,553 (-)NCBIGRCm37mm9NCBIm37
MGSCv361142,149,861 - 42,164,431 (-)NCBImm8
Celera1146,139,046 - 46,153,582 (-)NCBICelera
Cytogenetic Map11A5NCBI
cM Map1125.03NCBI
Gabra6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540815,464,368 - 15,480,330 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540815,464,426 - 15,479,653 (+)NCBIChiLan1.0ChiLan1.0
GABRA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15163,767,304 - 163,784,334 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5163,767,304 - 163,784,331 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05157,072,915 - 157,089,994 (+)NCBIMhudiblu_PPA_v0panPan3
GABRA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1449,208,691 - 49,225,754 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl449,208,605 - 49,226,212 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha449,099,501 - 49,116,828 (-)NCBI
ROS_Cfam_1.0449,639,863 - 49,657,617 (-)NCBI
UMICH_Zoey_3.1449,446,978 - 49,464,698 (-)NCBI
UNSW_CanFamBas_1.0449,579,983 - 49,597,659 (-)NCBI
UU_Cfam_GSD_1.0450,103,326 - 50,121,062 (-)NCBI
Gabra6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213103,533,076 - 103,548,851 (-)NCBI
SpeTri2.0NW_0049365151,982,415 - 1,997,740 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GABRA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1661,856,212 - 61,872,359 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11661,855,698 - 61,872,503 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21667,083,554 - 67,100,297 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GABRA6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12364,020,770 - 64,038,419 (+)NCBI
ChlSab1.1 Ensembl2364,021,842 - 64,039,563 (+)Ensembl
Gabra6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473327,910,692 - 27,926,104 (-)NCBI

Position Markers
RH138854  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01027,849,992 - 27,850,110NCBIRnor6.0
Rnor_5.01027,694,175 - 27,694,293UniSTSRnor5.0
RGSC_v3.41027,475,805 - 27,475,923UniSTSRGSC3.4
Celera1026,325,231 - 26,325,349UniSTS
RH 3.4 Map10279.9UniSTS
Cytogenetic Map10q21UniSTS
X51986  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01027,847,869 - 27,847,978NCBIRnor6.0
Rnor_5.01027,692,052 - 27,692,161UniSTSRnor5.0
RGSC_v3.41027,473,682 - 27,473,791UniSTSRGSC3.4
Celera1026,323,108 - 26,323,217UniSTS
Cytogenetic Map10q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129592136Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135538813Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10622909575983805Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10622928936185929Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10752145052521450Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101263951357639513Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101537547462469074Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101646873661468736Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101824639453637634Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101940281464402814Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102170776664648311Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102240281738204229Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102386101566539843Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102488408447487910Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102723753064648311Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat


Related Rat Strains
The following Strains have been annotated to Gabra6
ANT

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:74
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000004877
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 reproductive system respiratory system appendage
High
Medium 14
Low 1 1 1 12 2 1
Below cutoff 6 12 7 9 7 6 6 15 13 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004877   ⟹   ENSRNOP00000004877
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1027,847,439 - 27,862,868 (-)Ensembl
RefSeq Acc Id: NM_021841   ⟹   NP_068613
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21026,811,222 - 26,825,397 (-)NCBI
Rnor_6.01027,848,258 - 27,862,506 (-)NCBI
Rnor_5.01027,691,630 - 27,706,971 (-)NCBI
RGSC_v3.41027,474,071 - 27,489,074 (-)RGD
Celera1026,323,497 - 26,337,672 (-)RGD
Sequence:
RefSeq Acc Id: XM_006246128   ⟹   XP_006246190
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21026,810,411 - 26,825,768 (-)NCBI
Rnor_6.01027,847,447 - 27,862,896 (-)NCBI
Rnor_5.01027,691,630 - 27,706,971 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767636   ⟹   XP_008765858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01027,847,447 - 27,861,305 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_068613   ⟸   NM_021841
- Peptide Label: precursor
- UniProtKB: P30191 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006246190   ⟸   XM_006246128
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765858   ⟸   XM_008767636
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000004877   ⟸   ENSRNOT00000004877
Protein Domains
Neur_chan_LBD   Neur_chan_memb

Transcriptome

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

Promoters
RGD ID:13697110
Promoter ID:EPDNEW_R7635
Type:single initiation site
Name:Gabra6_1
Description:gamma-aminobutyric acid type A receptor alpha 6 subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01027,862,789 - 27,862,849EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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
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)
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)
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
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/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
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 (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
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
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
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
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
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 (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
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)
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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
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)
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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/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
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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 (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
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 (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 (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 (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61861 AgrOrtholog
Ensembl Genes ENSRNOG00000003569 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004877 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004877 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.70.170.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GABAA/Glycine_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GABAAa_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GABBAa6_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_lig-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_channel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neuro-gated_channel_TM_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotrans-gated_channel_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurotransmitter_ion_chnl_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29708 UniProtKB/Swiss-Prot
NCBI Gene 29708 ENTREZGENE
PANTHER PTHR18945 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Neur_chan_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neur_chan_memb UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gabra6 PhenoGen
PRINTS GABAARALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GABAARALPHA6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GABAARECEPTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NRIONCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NEUROTR_ION_CHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF63712 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs LIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6G3_RAT UniProtKB/TrEMBL
  GBRA6_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-06 Gabra6  gamma-aminobutyric acid type A receptor subunit alpha6  Gabra6  gamma-aminobutyric acid type A receptor alpha 6 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-11 Gabra6  gamma-aminobutyric acid type A receptor alpha 6 subunit  Gabra6  gamma-aminobutyric acid (GABA) A receptor, alpha 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-04 Gabra6  gamma-aminobutyric acid (GABA) A receptor, alpha 6  Gabra6  gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Gabra6  gamma-aminobutyric acid (GABA-A) receptor, subunit alpha 6    gamma-aminobutyric acid A receptor, alpha 6  Name updated 1299863 APPROVED
2002-06-10 Gabra6  gamma-aminobutyric acid A receptor, alpha 6      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression differentially expressed in the central nervous system 61594