Slc6a12 (solute carrier family 6 member 12)

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 and intracellular water homeostasis. Predicted to be located in basolateral plasma membrane. Predicted to be active in cell projection and plasma 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

Alliance Orthologs

More Info

more info ...

Allele / Splice:

Slc6a12^em1Mcwi

Genetic Models:

SS-Slc6a12^em1Mcwi

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Annotation category: suggests misassembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	156,257,518 - 156,275,870 (+)	NCBI		GRCr8
mRatBN7.2	4	154,585,386 - 154,603,750 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	154,585,500 - 154,603,750 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	160,851,569 - 160,869,938 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	156,635,049 - 156,653,409 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	155,258,488 - 155,276,847 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	153,921,199 - 153,941,333 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	153,921,115 - 153,941,391 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	221,009,224 - 221,029,242 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	157,781,178 - 157,800,038 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	158,026,113 - 158,044,974 (+)	NCBI
Celera	4	143,424,065 - 143,442,410 (+)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Hyperphosphatemic Familial Tumoral Calcinosis 1 (ISO)

Neoplasm Invasiveness (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-pilocarpine (ISO)

(+)-schisandrin B (EXP)

(1->4)-beta-D-glucan (ISO)

(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)

2-palmitoylglycerol (ISO)

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 A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bleomycin A2 (EXP)

cantharidin (ISO)

carbon nanotube (ISO)

chlorpyrifos (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)

hexadecanoic acid (ISO)

hydrazine (EXP)

inulin (ISO)

leflunomide (ISO)

lipopolysaccharide (ISO)

methapyrilene (ISO)

methidathion (ISO)

methoxychlor (EXP)

myxothiazol (ISO)

nefazodone (EXP)

ozone (EXP)

paracetamol (ISO)

paraquat (EXP)

perfluorohexanesulfonic acid (ISO)

perfluorooctane-1-sulfonic acid (EXP,ISO)

pioglitazone (ISO)

pirinixic acid (EXP,ISO)

quercetin (ISO)

rifampicin (ISO)

rotenone (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

senecionine (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium chloride (ISO)

succimer (ISO)

testosterone (EXP)

tetrachloromethane (EXP,ISO)

Theaflavin 3,3'-digallate (ISO)

thioacetamide (EXP)

titanium dioxide (EXP,ISO)

triclosan (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

troglitazone (ISO)

valdecoxib (EXP)

valproic acid (ISO)

XL147 (ISO)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

amino acid transport (IBA)

cellular hyperosmotic response (IEP)

gamma-aminobutyric acid transport (IEA,ISO,ISS)

glycine betaine transport (ISO,ISS)

intracellular water homeostasis (IDA)

monocarboxylic acid transport (ISO)

neurotransmitter transport (IEA,TAS)

response to kainic acid (IEP)

sodium ion transmembrane transport (IBA)

Cellular Component

basolateral plasma membrane (IEA,ISO,ISS)

cell projection (IBA)

lateral plasma membrane (IEA)

plasma membrane (IBA,ISO,ISS)

Molecular Function

gamma-aminobutyric acid:sodium:chloride symporter activity (IBA,IEA,ISO,ISS,TAS)

monocarboxylic acid transmembrane transporter activity (ISO)

protein binding (ISO)

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	PMID:35933616

Genomics

Comparative Map Data

Slc6a12
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	156,257,518 - 156,275,870 (+)	NCBI		GRCr8
mRatBN7.2	4	154,585,386 - 154,603,750 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	154,585,500 - 154,603,750 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	160,851,569 - 160,869,938 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	156,635,049 - 156,653,409 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	155,258,488 - 155,276,847 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	153,921,199 - 153,941,333 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	153,921,115 - 153,941,391 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	221,009,224 - 221,029,242 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	157,781,178 - 157,800,038 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	158,026,113 - 158,044,974 (+)	NCBI
Celera	4	143,424,065 - 143,442,410 (+)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

SLC6A12
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	183,848 - 214,157 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	190,077 - 214,570 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	299,247 - 323,323 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	169,513 - 192,753 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	169,512 - 192,759	NCBI
Celera	12	1,907,867 - 1,932,231 (-)	NCBI		Celera
Cytogenetic Map	12	p13.33	NCBI
HuRef	12	151,965 - 176,483 (-)	NCBI		HuRef
CHM1_1	12	298,191 - 322,361 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	179,876 - 211,078 (-)	NCBI		T2T-CHM13v2.0

Slc6a12
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	121,319,533 - 121,342,732 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	121,320,035 - 121,342,734 (+)	Ensembl		GRCm39 Ensembl
GRCm38	6	121,342,574 - 121,365,773 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	121,343,076 - 121,365,775 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	121,296,715 - 121,315,791 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	121,312,316 - 121,331,392 (+)	NCBI		MGSCv36	mm8
Celera	6	123,182,872 - 123,201,958 (+)	NCBI		Celera
Cytogenetic Map	6	F1	NCBI
cM Map	6	57.25	NCBI

Slc6a12
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955454	6,948,664 - 6,974,425 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955454	6,946,486 - 6,970,247 (+)	NCBI	ChiLan1.0	ChiLan1.0

SLC6A12
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	5,672,278 - 5,698,978 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	5,669,013 - 5,695,736 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	247,905 - 274,518 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	224,566 - 249,340 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	224,566 - 249,202 (-)	Ensembl	panpan1.1		panPan2

SLC6A12
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	42,270,427 - 42,301,874 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	42,270,448 - 42,336,464 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	4,389,231 - 4,413,912 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	42,628,605 - 42,656,421 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	42,628,606 - 42,655,432 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	42,569,709 - 42,594,385 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	42,541,235 - 42,565,923 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	3,749,203 - 3,773,888 (+)	NCBI		UU_Cfam_GSD_1.0

Slc6a12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	108,768,079 - 108,796,759 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936606	384,124 - 411,698 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936606	387,342 - 412,684 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLC6A12
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	67,550,289 - 67,572,588 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	67,550,285 - 67,573,858 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	69,838,027 - 69,861,857 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SLC6A12
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	192,590 - 223,809 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	192,398 - 215,991 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666063	8,120,189 - 8,148,179 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Slc6a12
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624735	8,445,405 - 8,468,083 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624735	8,441,046 - 8,469,611 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Slc6a12
112 total Variants

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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	109866907	167139601	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
631683	Bp116	Blood pressure QTL 116		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	124303370	169303370	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131730738	167139601	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	144639524	182687754	Rat
6478760	Anxrr45	Anxiety related response QTL 45		0.06717	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
6478763	Anxrr46	Anxiety related response QTL 46		0.07428	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	124778595	169778595	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	138503169	173369699	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	144639524	182687754	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	144639524	182687754	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	131730738	167139601	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	146565735	175236377	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	123143783	168143783	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	125590636	170590636	Rat
7207480	Bss105	Bone structure and strength QTL 105	8.1		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	4	109827074	154827074	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	138503169	179293946	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	119428175	157578333	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	85379421	167139601	Rat
1549827	Scl46	Serum cholesterol level QTL 46	3.5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	132396220	177396220	Rat
1549832	Bss3	Bone structure and strength QTL 3	11		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	4	109827074	154827074	Rat
1581574	Eae20	Experimental allergic encephalomyelitis QTL 20	7.8		nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	153031106	158841762	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	83428419	177635233	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	4	135699135	180699135	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	138503169	173369699	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	132642577	167139601	Rat
61446	Coreg2	Compensatory renal growth QTL 2	3.5		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	4	148423102	157580971	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	132422778	177422778	Rat
2303623	Vencon2	Ventilatory control QTL 2	3.8		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	4	135204660	180204660	Rat
1331759	Hrtrt13	Heart rate QTL 13	3.54628		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	110275411	168266883	Rat
724535	Cm18	Cardiac mass QTL 18	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	4	118856416	163856416	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	126395976	167139601	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	114627026	159627026	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	137755016	181392681	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	145568712	182687754	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	147278504	167139601	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	93308457	167139447	Rat
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	148090542	168069246	Rat

Markers in Region

RH142311

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	154,603,611 - 154,603,761 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	153,941,195 - 153,941,344	NCBI	Rnor6.0
Rnor_5.0	4	221,029,104 - 221,029,253	UniSTS	Rnor5.0
RGSC_v3.4	4	157,799,900 - 157,800,049	UniSTS	RGSC3.4
Celera	4	143,442,272 - 143,442,421	UniSTS
Cytogenetic Map	4	q42	UniSTS

Genetic Models

This gene Slc6a12 is modified in the following models/strains:

SS-Slc6a12^em1Mcwi

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017335	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229573	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U28927	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000018821 ⟹ ENSRNOP00000018821

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	154,585,500 - 154,603,750 (+)	Ensembl
Rnor_6.0 Ensembl	4	153,921,115 - 153,941,391 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000089482 ⟹ ENSRNOP00000071605

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	153,921,900 - 153,940,963 (+)	Ensembl

RefSeq Acc Id:

NM_017335 ⟹ NP_059031

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	156,257,518 - 156,275,870 (+)	NCBI
mRatBN7.2	4	154,585,386 - 154,603,750 (+)	NCBI
Rnor_6.0	4	153,921,199 - 153,941,333 (+)	NCBI
Rnor_5.0	4	221,009,224 - 221,029,242 (+)	NCBI
RGSC_v3.4	4	157,781,178 - 157,800,038 (+)	RGD
Celera	4	143,424,065 - 143,442,410 (+)	RGD

Sequence:

show sequence

AGTGTACTGGAGATCTGGACAGAAGGGCCAGCTGGAGTGGTGGCCGGCTGTAGAGATCAAAAGG
GATCTGAGCTATAATGGGGTTCTAATCACAGCTCTACCCCTGGGTGGTGTTGTGCAAGTCTCTG
ACCCCTGAAAGCCTGCTCTGTCTGTTGCTTTGTCTGCCGAAGACTGTGTGCAAGTCTCTGACCC
CTGAAAGCCTGCTCTGTCTGTTGCTTTGTCTGCCGAAGACTTGGCAAGCTAGGATCTGCTCCCT
GTTGGCTCAGCCCATAACTCTGAGAGCAGACTGTCACTTTAGATAGAAATGTCATCGGGAGCTT
GGGAAGAAAGGGTCTCCCTCTCCAGTATGGACAGAAAGGTTACAGTCCATGAAGATGGGTGTCC
TGTGGTCTCTTGGGTCCCTGAGGAGGGAGAGATGATGGACCAGAAAGACAAGGACCAGGTGAAG
GATCGAGGCCAATGGACCAACAAGATGGAGTTCGTACTGTCAGTGGCGGGAGAGATCATTGGCT
TAGGCAACGTCTGGAGGTTTCCCTATCTCTGCTACAAGAACGGGGGAGGAGCCTTCTTCATCCC
CTACTTCATCTTCTTCTTCAGCTGTGGTATCCCAGTGTTCTTCCTGGAGGTGGCACTGGGTCAG
TATAGCAGCCAGGGGAGTGTTACTGCTTGGAGGAAGATCTGTCCCCTTCTCCAAGGCATTGGCA
TGGCATCTGTGGTCATCGAGTCTTATTTGAACATCTACTACATCATCATCCTTGCCTGGGCTCT
CTTCTACCTGTTCAGCTCCTTCACCTGGGAGCTTCCCTGGACAACCTGCACCAACTCCTGGAAC
ACAGAACATTGCGTGGACTTTCTGAACTACTCATCGACCAGAGCCGCAAGCTACTCTGAGAACT
TCACCTCACCAGTCATGGAATTCTGGGAGAGACGGGTTTTGGGTATTACATCAGGCATCCATGA
CCTGGGGTCCCTGCGCTGGGAGCTGGCCCTGTGCCTCCTGCTCGCCTGGATCATCTGCTACTTC
TGCATCTGGAAGGGAGTCAAGTCCACGGGCAAGGTTGTTTACTTCACAGCCACTTTTCCCTACC
TGATGCTGATTATTCTTCTGATCCGGGGTGTTACCCTTCCTGGAGCCTACCAGGGCATCGTCTT
CTACCTGAAGCCAGACTTGCTCCGCCTCAAGGACCCCCAGGTGTGGATGGATGCGGGCACCCAG
ATCTTCTTTTCCTTTGCCATCTGCCAGGGGTGCCTCACGGCCCTGGGCAGCTACAACAAGTACC
ACAACAACTGCTACAGGGACTCCATCGCCCTCTGCTTCCTGAACAGTGCCACCAGCTTCGTGGC
TGGTTTTGTTGTCTTCTCCATCCTGGGCTTCATGGCTCAGGAGCAGGGCGTGCCCATTTCTGAA
GTGGCTGAGTCAGGTCCTGGACTGGCTTTCATTGCCTTCCCCAAAGCAGTGACGATGATGCCTT
TGTCCCAGCTGTGGTCCTGCCTCTTCTTCCTCATGCTCCTATTTCTAGGGCTGGACAGCCAGTT
CGTCTGTATGGAGTGCCTGGTCACTGCTTCCATGGATATGTTTCCTCAGCAGCTCCGAAAGAGA
GGCCGGCGCGAGCTGCTGATCCTCGCAGTTGCTATCGTGTGCTACTTGATGGGGCTCCTTCTGG
TCACTGAGGGTGGGATGTACATTTTCCAGCTCTTTGACTACTACGCCTCCAGCGGAATATGCCT
ACTCTTCCTCTCCTTGTTTGAGGTCATCTGCATTGGCTGGGTGTACGGGGCGGATCGTTTCTAT
GACAACGTGGAGGACATGATTGGCTATCGGCCATGGCCCTTGGTGAAGATCTCTTGGCTCTTCC
TGACCCCTGGTCTTTGCCTGGCCACCTTCTTCTTCTCCTTGAGCAAGTATACACCTCTCAAATA
CAACAATGTCTACATATACCCTTCTTGGGGATACTCCATTGGATGGCTCTTGGCTTTTTCCTCC
ATGGCCTGTGTACCGCTCTTTATTATCATCACCCTCCTGAAGACCCAGGGCTCCTTCAAGAAGC
GCCTTCAAAGACTCATCACGCCAGATCCCAGTCTGCCCCAGCCAGGGAGGCGTTCACCTCAGGA
TGGCTCCTCTGCTCAAAACTGTTCGACCTCTCCAGTCAAGCAAGAACTCATTGCCTGGGAGAAG
GAGACGCATTTGTAGGGAGTGCCAGAGGCCAGGTAACTCCAGAGCCAGGAACCTGGTCAAGGCT
AGCTCCTCCCAGGGTGAACCTCTCTTCCACCCTGTTGAGACCTCCCAGGTCTCTGGACACCCCT
GCTGGTCTTCGTTTGGCTGGGACAGCCTGTCACCTACCAGTCCTTTCCAGATGTGCTCCAGGAA
TCTGTTTGCCAAGACTTTTGAACTCAATGTCCTGACTTTTTGGATTTAAAAAAATGAAGAATCA
GAAAGGCAAAGTGATATTTTCAAGGTCATGCAGCCTTGCAGAGCCCAAGACCTTCCTTGGACTT
GCTGCTCTCTGCTGAGGAGAACCTCCAGCCTCACCCCTGCAGCAGTTAACAAGCCTGTGTGGAT
C

hide 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
Ensembl Protein	ENSRNOP00000018821
	ENSRNOP00000018821.3
GenBank Protein	P48056	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_059031 ⟸ NM_017335

- UniProtKB:

P48056 (UniProtKB/Swiss-Prot), A6ILC6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSGAWEERVSLSSMDRKVTVHEDGCPVVSWVPEEGEMMDQKDKDQVKDRGQWTNKMEFVLSVA
GEIIGLGNVWRFPYLCYKNGGGAFFIPYFIFFFSCGIPVFFLEVALGQYSSQGSVTAWRKICPL
LQGIGMASVVIESYLNIYYIIILAWALFYLFSSFTWELPWTTCTNSWNTEHCVDFLNYSSTRAA
SYSENFTSPVMEFWERRVLGITSGIHDLGSLRWELALCLLLAWIICYFCIWKGVKSTGKVVYFT
ATFPYLMLIILLIRGVTLPGAYQGIVFYLKPDLLRLKDPQVWMDAGTQIFFSFAICQGCLTALG
SYNKYHNNCYRDSIALCFLNSATSFVAGFVVFSILGFMAQEQGVPISEVAESGPGLAFIAFPKA
VTMMPLSQLWSCLFFLMLLFLGLDSQFVCMECLVTASMDMFPQQLRKRGRRELLILAVAIVCYL
MGLLLVTEGGMYIFQLFDYYASSGICLLFLSLFEVICIGWVYGADRFYDNVEDMIGYRPWPLVK
ISWLFLTPGLCLATFFFSLSKYTPLKYNNVYIYPSWGYSIGWLLAFSSMACVPLFIIITLLKTQ
GSFKKRLQRLITPDPSLPQPGRRSPQDGSSAQNCSTSPVKQELIAWEKETHL

hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	153,921,197 - 153,921,257	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620255	AgrOrtholog
BioCyc Gene	G2FUF-43177	BioCyc
Ensembl Genes	ENSRNOG00000013547	Ensembl, ENTREZGENE, 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
	SODIUM- AND CHLORIDE-DEPENDENT BETAINE TRANSPORTER	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
RatGTEx	ENSRNOG00000013547	RatGTEx
Superfamily-SCOP	SSF161070	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JSN3_RAT	UniProtKB/TrEMBL
	A6ILC6	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

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