Slc6a1 (solute carrier family 6 member 1) - Rat Genome Database

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Gene: Slc6a1 (solute carrier family 6 member 1) Rattus norvegicus
Analyze
Symbol: Slc6a1
Name: solute carrier family 6 member 1
RGD ID: 620533
Description: Exhibits gamma-aminobutyric acid:sodium symporter activity and identical protein binding activity. Involved in several processes, including gamma-aminobutyric acid import; negative regulation of GABAergic synaptic transmission; and positive regulation of gamma-aminobutyric acid secretion. Localizes to several cellular components, including GABA-ergic synapse; cell surface; and integral component of synaptic membrane. Used to study brain ischemia. Biomarker of cerebral infarction; epilepsy; temporal lobe epilepsy; and withdrawal disorder. Orthologous to human SLC6A1 (solute carrier family 6 member 1); INTERACTS WITH (+)-pilocarpine; 17alpha-ethynylestradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GABA transporter protein; Gabt1; GAT-1; Gat1; sodium- and chloride-dependent GABA transporter 1; solute carrier family 6 (neurotransmitter transporter), member 1; solute carrier family 6 (neurotransmitter transporter, GABA), member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24147,448,961 - 147,482,295 (+)NCBI
Rnor_6.0 Ensembl4146,276,862 - 146,292,213 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04146,258,842 - 146,292,176 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04209,552,452 - 209,585,794 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44150,249,867 - 150,265,186 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14150,494,707 - 150,510,027 (+)NCBI
Celera4136,018,664 - 136,033,983 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Alele PE and Devaud LL, Alcohol Clin Exp Res. 2005 Jun;29(6):1027-34.
2. Allen NJ, etal., J Neurosci. 2004 Apr 14;24(15):3837-49.
3. Calcagnotto ME, etal., J Neurosci. 2002 Sep 1;22(17):7596-605.
4. Deken SL, etal., Nat Neurosci. 2000 Oct;3(10):998-1003.
5. Frahm C, etal., J Comp Neurol. 2004 Oct 11;478(2):176-88.
6. Fueta Y, etal., Neuroscience. 2004;124(3):593-603.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Gonzalez B, etal., Neuropharmacology. 2006 Jul;51(1):154-9. Epub 2006 May 30.
10. Guastella J, etal., Science 1990 Sep 14;249(4974):1303-6.
11. Hu J and Quick MW, Neuropharmacology. 2007 Oct 7;.
12. Linetska MV, etal., Neurochem Int. 2004 Apr;44(5):303-12.
13. Ma YH, etal., Cell Res. 2000 Dec;10(4):303-10.
14. Marchionni I, etal., J Physiol. 2007 Jun 1;581(Pt 2):515-28. Epub 2007 Feb 22.
15. Mari SA, etal., Cell Mol Life Sci. 2006 Jan;63(1):100-11.
16. Melone M, etal., Brain Struct Funct. 2015 Mar;220(2):885-97. doi: 10.1007/s00429-013-0690-8. Epub 2013 Dec 25.
17. Melone M, etal., Front Neuroanat. 2014 Jul 25;8:72. doi: 10.3389/fnana.2014.00072. eCollection 2014.
18. MGD data from the GO Consortium
19. Morrow BA, etal., J Neurosci. 2003 Jun 15;23(12):5227-34.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. OMIM Disease Annotation Pipeline
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Schmid JA, etal., J Biol Chem. 2001 Feb 9;276(6):3805-10. Epub 2000 Nov 8.
26. Schmitt U and Hiemke C, Behav Brain Res. 2002 Jul 18;133(2):391-4.
27. Schmitt U, etal., J Neural Transm. 2002 May;109(5-6):871-80.
28. Scholze P, etal., J Biol Chem 2002 Nov 15;277(46):43682-90.
29. Shibutani M, etal., Toxicology. 2005 Mar 1;208(1):35-48.
30. Soragna A, etal., Cell Mol Life Sci. 2005 Dec;62(23):2877-85.
31. Struzynska L and Sulkowski G, J Inorg Biochem. 2004 Jun;98(6):951-8.
32. Ueda Y, etal., Brain Res. 2007 Jun 2;1151:55-61. Epub 2007 Mar 13.
33. Wang D and Quick MW, J Biol Chem. 2005 May 13;280(19):18703-9. Epub 2005 Mar 18.
34. Wang D, etal., Mol Pharmacol. 2003 Oct;64(4):905-13.
35. Xu YF, etal., J Neurosci Res. 2007 Oct 5;.
36. Zhu XM and Ong WY, J Neurosci Res. 2004 Aug 1;77(3):402-9.
Additional References at PubMed
PMID:9169433   PMID:10973981   PMID:11453549   PMID:12381817   PMID:12482883   PMID:12764157   PMID:15234345   PMID:15479642   PMID:17724084   PMID:19363027   PMID:21131297   PMID:22871113  
PMID:23443081   PMID:24359690   PMID:25798861   PMID:26390912   PMID:30790582  


Genomics

Comparative Map Data
Slc6a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24147,448,961 - 147,482,295 (+)NCBI
Rnor_6.0 Ensembl4146,276,862 - 146,292,213 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04146,258,842 - 146,292,176 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04209,552,452 - 209,585,794 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44150,249,867 - 150,265,186 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14150,494,707 - 150,510,027 (+)NCBI
Celera4136,018,664 - 136,033,983 (+)NCBICelera
Cytogenetic Map4q42NCBI
SLC6A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl310,992,186 - 11,039,247 (+)EnsemblGRCh38hg38GRCh38
GRCh38310,992,748 - 11,039,247 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37311,034,434 - 11,080,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36311,009,453 - 11,055,935 (+)NCBINCBI36hg18NCBI36
Build 34311,009,455 - 11,055,934NCBI
Celera310,969,866 - 11,016,381 (+)NCBI
Cytogenetic Map3p25.3ENTREZGENE
HuRef310,969,346 - 11,015,750 (+)NCBIHuRef
CHM1_1310,984,449 - 11,030,960 (+)NCBICHM1_1
Slc6a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396114,259,596 - 114,294,491 (+)NCBIGRCm39mm39
GRCm39 Ensembl6114,259,596 - 114,294,493 (+)Ensembl
GRCm386114,282,635 - 114,317,525 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6114,282,635 - 114,317,532 (+)EnsemblGRCm38mm10GRCm38
MGSCv376114,232,629 - 114,267,519 (+)NCBIGRCm37mm9NCBIm37
MGSCv366114,248,369 - 114,283,117 (+)NCBImm8
Celera6116,104,017 - 116,138,918 (+)NCBICelera
Cytogenetic Map6E3NCBI
Slc6a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542913,930,905 - 13,947,389 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542913,930,899 - 13,946,010 (+)NCBIChiLan1.0ChiLan1.0
SLC6A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1311,296,014 - 11,323,624 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl311,296,023 - 11,323,624 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0310,930,455 - 10,976,968 (+)NCBIMhudiblu_PPA_v0panPan3
SLC6A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1207,341,071 - 7,383,197 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl207,341,072 - 7,383,287 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha207,376,561 - 7,418,616 (-)NCBI
ROS_Cfam_1.0207,371,107 - 7,413,167 (-)NCBI
UMICH_Zoey_3.1207,087,370 - 7,129,439 (-)NCBI
UNSW_CanFamBas_1.0207,443,566 - 7,485,634 (-)NCBI
UU_Cfam_GSD_1.0207,415,545 - 7,457,611 (-)NCBI
Slc6a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494216,512,443 - 16,550,935 (+)NCBI
SpeTri2.0NW_0049366022,359,151 - 2,397,346 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1367,156,824 - 67,199,087 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11367,156,786 - 67,199,092 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21374,321,093 - 74,341,573 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12247,033,436 - 47,076,785 (+)NCBI
ChlSab1.1 Ensembl2247,033,467 - 47,078,844 (+)Ensembl
Slc6a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624943632,534 - 662,924 (-)NCBI

Position Markers
Gabt1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04146,291,854 - 146,292,134NCBIRnor6.0
Rnor_5.04209,585,472 - 209,585,752UniSTSRnor5.0
RGSC_v3.44150,264,866 - 150,265,146UniSTSRGSC3.4
Celera4136,033,663 - 136,033,943UniSTS
Cytogenetic Map4q42UniSTS
Slc6a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04146,283,137 - 146,284,023NCBIRnor6.0
Rnor_5.04209,576,755 - 209,577,641UniSTSRnor5.0
Celera4136,024,946 - 136,025,832UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120400597146942261Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105277348150277348Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106347236151347236Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486312589146942261Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4115372758150038284Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109636356154636356Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4105682594150682594Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109636356154636356Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)486312589147702403Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146086918168047091Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:347
Count of miRNA genes:183
Interacting mature miRNAs:249
Transcripts:ENSRNOT00000009705
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 68
Low 2 3 2 2 2 2 6 14 24 2 2
Below cutoff 3 26 26 13 12 13 6 6 8 16 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009705   ⟹   ENSRNOP00000009705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4146,276,862 - 146,292,213 (+)Ensembl
RefSeq Acc Id: NM_024371   ⟹   NP_077347
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24147,466,974 - 147,482,293 (+)NCBI
Rnor_6.04146,276,855 - 146,292,174 (+)NCBI
Rnor_5.04209,552,452 - 209,585,794 (+)NCBI
RGSC_v3.44150,249,867 - 150,265,186 (+)RGD
Celera4136,018,664 - 136,033,983 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237059   ⟹   XP_006237121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24147,448,961 - 147,482,295 (+)NCBI
Rnor_6.04146,258,842 - 146,292,176 (+)NCBI
Rnor_5.04209,552,452 - 209,585,794 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237060   ⟹   XP_006237122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04146,275,045 - 146,292,176 (+)NCBI
Rnor_5.04209,552,452 - 209,585,794 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_077347 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237121 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA63487 (Get FASTA)   NCBI Sequence Viewer  
  EDL91564 (Get FASTA)   NCBI Sequence Viewer  
  EDL91565 (Get FASTA)   NCBI Sequence Viewer  
  P23978 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_077347   ⟸   NM_024371
- UniProtKB: P23978 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237121   ⟸   XM_006237059
- Peptide Label: isoform X1
- UniProtKB: P23978 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237122   ⟸   XM_006237060
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000009705   ⟸   ENSRNOT00000009705

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 (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 (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/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 (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)
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
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
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/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
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 (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
Damaging Variants


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 150262153 150262154 T A snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620533 AgrOrtholog
Ensembl Genes ENSRNOG00000006527 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009705 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009705 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Na/ntran_symport UniProtKB/Swiss-Prot
  Na/ntran_symport_GABA_GAT1 UniProtKB/Swiss-Prot
  SNS_sf UniProtKB/Swiss-Prot
KEGG Report rno:79212 UniProtKB/Swiss-Prot
NCBI Gene 79212 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot
Pfam SNF UniProtKB/Swiss-Prot
PharmGKB SLC6A1 RGD
PhenoGen Slc6a1 PhenoGen
PRINTS GAT1TRNSPORT UniProtKB/Swiss-Prot
  NANEUSMPORT UniProtKB/Swiss-Prot
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot
UniProt P23978 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc6a1  solute carrier family 6 member 1  Slc6a1  solute carrier family 6 (neurotransmitter transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc6a1  solute carrier family 6 (neurotransmitter transporter), member 1  Slc6a1  solute carrier family 6 (neurotransmitter transporter, GABA), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Slc6a1  solute carrier family 6 (neurotransmitter transporter, GABA), member 1    GABA transporter protein  Name updated 1299863 APPROVED
2004-09-10 Slc6a1  GABA transporter protein  Gabt1    Symbol and Name updated 1299863 APPROVED
2002-08-07 Gabt1  GABA transporter protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_protein 599 amino acids with predicted molecular weight of 67 kDa 632739
gene_regulation sodium-and chloride-dependent, high affinity for GABA 632739