Slc6a13 (solute carrier family 6 member 13) - Rat Genome Database

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Gene: Slc6a13 (solute carrier family 6 member 13) Rattus norvegicus
Analyze
Symbol: Slc6a13
Name: solute carrier family 6 member 13
RGD ID: 620788
Description: Enables neurotransmitter binding activity and organic anion transmembrane transporter activity. Involved in neurotransmitter transport and organic anion transport. Located in plasma membrane. Orthologous to human SLC6A13 (solute carrier family 6 member 13); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GAT-2; sodium- and chloride-dependent GABA transporter 2; solute carrier family 6 (neurotransmitter transporter), member 13; solute carrier family 6 (neurotransmitter transporter, GABA), member 13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24154,539,246 - 154,577,784 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4154,540,468 - 154,576,152 (+)Ensembl
Rnor_6.04153,874,942 - 153,912,185 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4153,874,852 - 153,912,155 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04220,962,968 - 221,000,197 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44157,736,264 - 157,771,945 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14157,981,199 - 158,016,881 (+)NCBI
Celera4143,379,280 - 143,414,859 (+)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
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
alachlor  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcium silicate  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
coumarin  (EXP)
crocidolite asbestos  (ISO)
dioxygen  (ISO)
endosulfan  (EXP)
ethyl methanesulfonate  (ISO)
flavonoids  (EXP)
fluconazole  (EXP)
flutamide  (EXP)
furan  (EXP)
gamma-aminobutyric acid  (ISO)
graphite  (EXP)
GW 4064  (ISO)
hydralazine  (ISO)
leflunomide  (EXP)
Licochalcone B  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
Muraglitazar  (EXP)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
paracetamol  (ISO)
phenobarbital  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SCH 23390  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
succimer  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
tremolite asbestos  (ISO)
triadimefon  (EXP)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (EXP)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:19056867  


Genomics

Comparative Map Data
Slc6a13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24154,539,246 - 154,577,784 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4154,540,468 - 154,576,152 (+)Ensembl
Rnor_6.04153,874,942 - 153,912,185 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4153,874,852 - 153,912,155 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04220,962,968 - 221,000,197 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44157,736,264 - 157,771,945 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14157,981,199 - 158,016,881 (+)NCBI
Celera4143,379,280 - 143,414,859 (+)NCBICelera
Cytogenetic Map4q42NCBI
SLC6A13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812220,622 - 262,836 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12220,621 - 262,873 (-)EnsemblGRCh38hg38GRCh38
GRCh3712329,788 - 372,002 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612200,052 - 242,263 (-)NCBINCBI36hg18NCBI36
Build 3412200,051 - 242,263NCBI
Celera121,938,637 - 1,980,875 (-)NCBI
Cytogenetic Map12p13.33NCBI
HuRef12182,903 - 225,079 (-)NCBIHuRef
CHM1_112328,777 - 371,038 (-)NCBICHM1_1
T2T-CHM13v2.012217,551 - 259,667 (-)NCBI
Slc6a13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396121,277,184 - 121,314,680 (+)NCBIGRCm39mm39
GRCm39 Ensembl6121,277,186 - 121,314,692 (+)Ensembl
GRCm386121,300,288 - 121,337,721 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6121,300,227 - 121,337,733 (+)EnsemblGRCm38mm10GRCm38
MGSCv376121,250,314 - 121,287,736 (+)NCBIGRCm37mm9NCBIm37
MGSCv366121,265,915 - 121,303,337 (+)NCBImm8
Celera6123,134,593 - 123,173,892 (+)NCBICelera
Cytogenetic Map6F1NCBI
Slc6a13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554546,866,740 - 6,940,734 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554546,866,740 - 6,940,686 (+)NCBIChiLan1.0ChiLan1.0
SLC6A13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112255,141 - 296,926 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12255,141 - 296,926 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012279,434 - 334,226 (-)NCBIMhudiblu_PPA_v0panPan3
SLC6A13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12742,302,762 - 42,338,911 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2742,270,448 - 42,336,464 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha274,345,500 - 4,381,643 (+)NCBI
ROS_Cfam_1.02742,660,870 - 42,697,019 (-)NCBI
ROS_Cfam_1.0 Ensembl2742,660,893 - 42,694,550 (-)Ensembl
UMICH_Zoey_3.12742,601,961 - 42,637,965 (-)NCBI
UNSW_CanFamBas_1.02742,573,532 - 42,609,397 (-)NCBI
UU_Cfam_GSD_1.0273,705,273 - 3,741,637 (+)NCBI
Slc6a13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945108,728,385 - 108,767,931 (+)NCBI
SpeTri2.0NW_004936606416,170 - 455,720 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl567,577,197 - 67,612,681 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1567,574,149 - 67,617,513 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2569,865,018 - 69,905,417 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111223,912 - 274,499 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11223,793 - 264,719 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660638,072,317 - 8,116,503 (+)NCBIVero_WHO_p1.0


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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:58
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000018083
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 41 41 41 34 18
Low 30 6 2 3 3 28 17 26 5 3
Below cutoff 13 9 17 4 6 12 9 6 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018083   ⟹   ENSRNOP00000018083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4154,540,468 - 154,576,152 (+)Ensembl
Rnor_6.0 Ensembl4153,876,149 - 153,911,966 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079744   ⟹   ENSRNOP00000071638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4154,544,022 - 154,576,152 (+)Ensembl
Rnor_6.0 Ensembl4153,874,852 - 153,912,155 (+)Ensembl
RefSeq Acc Id: NM_133623   ⟹   NP_598307
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,540,468 - 154,576,152 (+)NCBI
Rnor_6.04153,876,149 - 153,911,966 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
RGSC_v3.44157,736,264 - 157,771,945 (+)RGD
Celera4143,379,280 - 143,414,859 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237218   ⟹   XP_006237280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,539,246 - 154,577,784 (+)NCBI
Rnor_6.04153,874,942 - 153,912,185 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237219   ⟹   XP_006237281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,539,335 - 154,577,784 (+)NCBI
Rnor_6.04153,874,946 - 153,912,185 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237220   ⟹   XP_006237282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,539,246 - 154,577,784 (+)NCBI
Rnor_6.04153,874,942 - 153,912,185 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237221   ⟹   XP_006237283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,539,337 - 154,577,784 (+)NCBI
Rnor_6.04153,874,946 - 153,912,185 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237222   ⟹   XP_006237284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,544,000 - 154,577,784 (+)NCBI
Rnor_6.04153,879,688 - 153,912,172 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006237223   ⟹   XP_006237285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,542,114 - 154,577,784 (+)NCBI
Rnor_6.04153,877,735 - 153,912,185 (+)NCBI
Rnor_5.04220,962,968 - 221,000,197 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106981   ⟹   XP_038962909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,539,246 - 154,573,149 (+)NCBI
RefSeq Acc Id: XM_039106982   ⟹   XP_038962910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,564,805 - 154,577,784 (+)NCBI
RefSeq Acc Id: XM_039106983   ⟹   XP_038962911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24154,568,052 - 154,577,784 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_598307   ⟸   NM_133623
- UniProtKB: P31646 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237280   ⟸   XM_006237218
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006237282   ⟸   XM_006237220
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006237281   ⟸   XM_006237219
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006237283   ⟸   XM_006237221
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006237285   ⟸   XM_006237223
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006237284   ⟸   XM_006237222
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000071638   ⟸   ENSRNOT00000079744
RefSeq Acc Id: ENSRNOP00000018083   ⟸   ENSRNOT00000018083
RefSeq Acc Id: XP_038962909   ⟸   XM_039106981
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038962910   ⟸   XM_039106982
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038962911   ⟸   XM_039106983
- Peptide Label: isoform X7

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P31646-F1-model_v2 AlphaFold P31646 1-602 view protein structure

Transcriptome

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

Promoters
RGD ID:13693364
Promoter ID:EPDNEW_R3888
Type:single initiation site
Name:Slc6a13_1
Description:solute carrier family 6 member 13
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_6.04153,875,005 - 153,875,065EPDNEW

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)
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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:620788 AgrOrtholog
BioCyc Gene G2FUF-43178 BioCyc
Ensembl Genes ENSRNOG00000012876 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018083 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071638 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018083 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079744 ENTREZGENE, UniProtKB/TrEMBL
InterPro Na/ntran_symport UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/ntran_symport_GABA_GAT2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171163 UniProtKB/Swiss-Prot
NCBI Gene 171163 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc6a13 PhenoGen
PRINTS GAT2TRNSPORT 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 A0A0G2K0Z3_RAT UniProtKB/TrEMBL
  P31646 ENTREZGENE
  R9PXV0_RAT UniProtKB/TrEMBL
  S6A13_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc6a13  solute carrier family 6 member 13  Slc6a13  solute carrier family 6 (neurotransmitter transporter), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc6a13  solute carrier family 6 (neurotransmitter transporter), member 13  Slc6a13  solute carrier family 6 (neurotransmitter transporter, GABA), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc6a13  solute carrier family 6 (neurotransmitter transporter, GABA), member 13      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Slc6a13  solute carrier family 6 (neurotransmitter transporter, GABA), member 13      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression protein found in glial cells in the gastrointestinal tract 730059
gene_expression mRNA expressed in brain, retina, and some peripheral tissues 727560
gene_protein Km for GABA approximately 10 microM 727560
gene_protein predicted protein contains 602 amino acid residues 727560