Slc6a12 (solute carrier family 6 member 12) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Slc6a12 (solute carrier family 6 member 12) Rattus norvegicus
Analyze
Symbol: Slc6a12
Name: solute carrier family 6 member 12
RGD ID: 620255
Description: Predicted to enable gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in cellular hyperosmotic response; cellular water homeostasis; and response to organic substance. Is integral component of membrane. Orthologous to human SLC6A12 (solute carrier family 6 member 12); INTERACTS WITH (+)-schisandrin B; (aminooxy)acetic acid; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Betaine/GABA transporter 1; BGT1; GABA transporter; GABA transporter 1; Gat1; na(+)/Cl(-) betaine/GABA transporter; RNU28927; sodium- and chloride-dependent betaine transporter; solute carrier family 6 (neurotransmitter transporter), member 12; solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12; vesicular GABA transporter; VGAT
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc6a12em1Mcwi  
Genetic Models: SS-Slc6a12em1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24154,585,386 - 154,603,750 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4154,585,500 - 154,603,750 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4160,851,569 - 160,869,938 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04156,635,049 - 156,653,409 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04155,258,488 - 155,276,847 (+)NCBIRnor_WKY
Rnor_6.04153,921,199 - 153,941,333 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4153,921,115 - 153,941,391 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04221,009,224 - 221,029,242 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44157,781,178 - 157,800,038 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14158,026,113 - 158,044,974 (+)NCBI
Celera4143,424,065 - 143,442,410 (+)NCBICelera
Cytogenetic Map4q42NCBI
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
(+)-pilocarpine  (ISO)
(+)-schisandrin B  (EXP)
(aminooxy)acetic acid  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
carbon nanotube  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazepam  (EXP)
dichlorine  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
endosulfan  (EXP)
fenthion  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP)
genistein  (ISO)
glycine betaine  (ISO)
hydrazine  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
methidathion  (ISO)
myxothiazol  (ISO)
nefazodone  (EXP)
ozone  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
quercetin  (ISO)
rifampicin  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium chloride  (ISO)
succimer  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
XL147  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. A liver-specific isoform of the betaine/GABA transporter in the rat: cDNA sequence and organ distribution. Burnham CE, etal., Biochim Biophys Acta 1996 Oct 2;1284(1):4-8.
2. Two discontinuous segments in the carboxyl terminus are required for membrane targeting of the rat gamma-aminobutyric acid transporter-1 (GAT1). Farhan H, etal., J Biol Chem 2004 Jul 2;279(27):28553-63. Epub 2004 Apr 08.
3. Possible expression of a particular gamma-aminobutyric acid transporter isoform responsive to upregulation by hyperosmolarity in rat calvarial osteoblasts. Fujimori S, etal., Eur J Pharmacol. 2006 Nov 21;550(1-3):24-32. Epub 2006 Sep 14.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Postnatal development of the vesicular GABA transporter in rat cerebral cortex. Minelli A, etal., Neuroscience 2003;117(2):337-46.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Passive water permeability of some wild type and mutagenized amino acid cotransporters of the SLC6/NSS family expressed in Xenopus laevis oocytes. Santacroce M, etal., Comp Biochem Physiol A Mol Integr Physiol. 2010 Apr 13.
12. Changes in GABA transporters in the rat hippocampus after kainate-induced neuronal injury: decrease in GAT-1 and GAT-3 but upregulation of betaine/GABA transporter BGT-1. Zhu XM and Ong WY, J Neurosci Res. 2004 Aug 1;77(3):402-9.
Additional References at PubMed
PMID:14663191   PMID:14761965   PMID:15229234   PMID:15649449   PMID:15668946   PMID:15778221   PMID:15936116   PMID:16378241   PMID:16616431   PMID:16861228   PMID:17298599   PMID:18512213  
PMID:19235900   PMID:19576516   PMID:20542084   PMID:20851161   PMID:21410779   PMID:21775701   PMID:21969376   PMID:22616751   PMID:23090943   PMID:23381899   PMID:23804087  


Genomics

Comparative Map Data
Slc6a12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24154,585,386 - 154,603,750 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4154,585,500 - 154,603,750 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4160,851,569 - 160,869,938 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04156,635,049 - 156,653,409 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04155,258,488 - 155,276,847 (+)NCBIRnor_WKY
Rnor_6.04153,921,199 - 153,941,333 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4153,921,115 - 153,941,391 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04221,009,224 - 221,029,242 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44157,781,178 - 157,800,038 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14158,026,113 - 158,044,974 (+)NCBI
Celera4143,424,065 - 143,442,410 (+)NCBICelera
Cytogenetic Map4q42NCBI
SLC6A12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812183,848 - 214,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12190,077 - 214,570 (-)EnsemblGRCh38hg38GRCh38
GRCh3712299,247 - 323,323 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612169,513 - 192,753 (-)NCBINCBI36Build 36hg18NCBI36
Build 3412169,512 - 192,759NCBI
Celera121,907,867 - 1,932,231 (-)NCBICelera
Cytogenetic Map12p13.33NCBI
HuRef12151,965 - 176,483 (-)NCBIHuRef
CHM1_112298,191 - 322,361 (-)NCBICHM1_1
T2T-CHM13v2.012186,072 - 211,078 (-)NCBIT2T-CHM13v2.0
Slc6a12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396121,319,533 - 121,342,732 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6121,320,035 - 121,342,734 (+)EnsemblGRCm39 Ensembl
GRCm386121,342,574 - 121,365,773 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6121,343,076 - 121,365,775 (+)EnsemblGRCm38mm10GRCm38
MGSCv376121,296,715 - 121,315,791 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366121,312,316 - 121,331,392 (+)NCBIMGSCv36mm8
Celera6123,182,872 - 123,201,958 (+)NCBICelera
Cytogenetic Map6F1NCBI
Slc6a12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554546,948,664 - 6,974,425 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554546,946,486 - 6,970,247 (+)NCBIChiLan1.0ChiLan1.0
SLC6A12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112224,566 - 249,340 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12224,566 - 249,202 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012247,905 - 274,518 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC6A12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12742,270,427 - 42,301,874 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2742,270,448 - 42,336,464 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha274,389,231 - 4,413,912 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02742,628,605 - 42,656,421 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2742,628,606 - 42,655,432 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12742,569,709 - 42,594,385 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02742,541,235 - 42,565,923 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0273,749,203 - 3,773,888 (+)NCBIUU_Cfam_GSD_1.0
Slc6a12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945108,768,079 - 108,796,759 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936606387,342 - 412,684 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl567,550,289 - 67,572,588 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1567,550,285 - 67,573,858 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2569,838,027 - 69,861,857 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111192,590 - 223,809 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11192,398 - 215,991 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660638,120,189 - 8,148,179 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc6a12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247358,445,405 - 8,468,083 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247358,441,046 - 8,469,611 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
RH142311  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24154,603,611 - 154,603,761 (+)MAPPERmRatBN7.2
Rnor_6.04153,941,195 - 153,941,344NCBIRnor6.0
Rnor_5.04221,029,104 - 221,029,253UniSTSRnor5.0
RGSC_v3.44157,799,900 - 157,800,049UniSTSRGSC3.4
Celera4143,442,272 - 143,442,421UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
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)4110870972155870972Rat
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)4110870972155870972Rat
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)4114627026159627026Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
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)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
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)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat


Genetic Models
This gene Slc6a12 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:334
Count of miRNA genes:184
Interacting mature miRNAs:211
Transcripts:ENSRNOT00000018821
Prediction methods:Microtar, 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 23 23 23 3
Low 2 27 18 19 18 32 20 14 10
Below cutoff 1 41 7 5 6 38 12 25 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018821   ⟹   ENSRNOP00000018821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4154,585,500 - 154,603,750 (+)Ensembl
Rnor_6.0 Ensembl4153,921,115 - 153,941,391 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089482   ⟹   ENSRNOP00000071605
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4153,921,900 - 153,940,963 (+)Ensembl
RefSeq Acc Id: NM_017335   ⟹   NP_059031
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,585,386 - 154,603,750 (+)NCBI
Rnor_6.04153,921,199 - 153,941,333 (+)NCBI
Rnor_5.04221,009,224 - 221,029,242 (+)NCBI
RGSC_v3.44157,781,178 - 157,800,038 (+)RGD
Celera4143,424,065 - 143,442,410 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_059031 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC52867 (Get FASTA)   NCBI Sequence Viewer  
  EDM02013 (Get FASTA)   NCBI Sequence Viewer  
  P48056 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_059031   ⟸   NM_017335
- UniProtKB: P48056 (UniProtKB/Swiss-Prot),   A0A0G2JSN3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018821   ⟸   ENSRNOT00000018821
RefSeq Acc Id: ENSRNOP00000071605   ⟸   ENSRNOT00000089482

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P48056-F1-model_v2 AlphaFold P48056 1-614 view protein structure

Transcriptome

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

Promoters
RGD ID:13693365
Promoter ID:EPDNEW_R3889
Type:initiation region
Name:Slc6a12_1
Description:solute carrier family 6 member 12
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_6.04153,921,197 - 153,921,257EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
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
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
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
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
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
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620255 AgrOrtholog
BioCyc Gene G2FUF-43177 BioCyc
Ensembl Genes ENSRNOG00000013547 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018821 ENTREZGENE
  ENSRNOP00000018821.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018821 ENTREZGENE
  ENSRNOT00000018821.5 UniProtKB/TrEMBL
InterPro Na/ntran_symport UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/ntran_symport_betaine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50676 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 50676 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SLC6A12 RGD
PhenoGen Slc6a12 PhenoGen
PRINTS BETTRANSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NANEUSMPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSN3 ENTREZGENE, UniProtKB/TrEMBL
  P48056 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-12-07   solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12  Slc6a12  GABA transporter  Name updated 1299863 APPROVED
2004-09-10 Slc6a12  GABA transporter  RNU28927    Symbol and Name updated 1299863 APPROVED
2002-08-07 RNU28927  GABA transporter      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in brain, spleen, liver, lung, and kidney 633749