Slc12a6 (solute carrier family 12, member 6) - Rat Genome Database

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Gene: Slc12a6 (solute carrier family 12, member 6) Rattus norvegicus
Analyze
Symbol: Slc12a6
Name: solute carrier family 12, member 6
RGD ID: 1311335
Description: Predicted to have ammonium transmembrane transporter activity; potassium:chloride symporter activity; and protein kinase binding activity. Predicted to be involved in several processes, including cellular hypotonic salinity response; inorganic ion homeostasis; and inorganic ion transmembrane transport. Predicted to localize to axon and basolateral plasma membrane. Human ortholog(s) of this gene implicated in agenesis of the corpus callosum with peripheral neuropathy. Orthologous to human SLC12A6 (solute carrier family 12 member 6); PARTICIPATES IN amiloride pharmacodynamics pathway; bendroflumethiazide pharmacodynamics pathway; bumetanide pharmacodynamics pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: furosemide-sensitive KCl cotransporter 3; Kcc3; LOC362189; LOC691209; similar to Solute carrier family 12 member 6 (Electroneutral potassium-chloride cotransporter 3) (K-Cl cotransporter 3); solute carrier family 12 member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2399,071,577 - 99,170,266 (+)NCBI
Rnor_6.0 Ensembl3103,753,238 - 103,852,686 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03103,752,213 - 103,852,686 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03110,347,112 - 110,446,527 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4398,110,547 - 98,212,242 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1398,005,593 - 98,106,019 (+)NCBI
Celera398,058,005 - 98,155,735 (+)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:10187864   PMID:11246162   PMID:12657561   PMID:15533301   PMID:16048901   PMID:16872584   PMID:18178552   PMID:20691666   PMID:22732406   PMID:22776998   PMID:24089410   PMID:24393035  
PMID:27782176  


Genomics

Comparative Map Data
Slc12a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2399,071,577 - 99,170,266 (+)NCBI
Rnor_6.0 Ensembl3103,753,238 - 103,852,686 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03103,752,213 - 103,852,686 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03110,347,112 - 110,446,527 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4398,110,547 - 98,212,242 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1398,005,593 - 98,106,019 (+)NCBI
Celera398,058,005 - 98,155,735 (+)NCBICelera
Cytogenetic Map3q35NCBI
SLC12A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1534,229,784 - 34,338,060 (-)EnsemblGRCh38hg38GRCh38
GRCh381534,229,784 - 34,338,057 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371534,521,985 - 34,630,258 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361532,309,489 - 32,417,557 (-)NCBINCBI36hg18NCBI36
Build 341532,312,957 - 32,398,222NCBI
Celera1511,324,764 - 11,432,905 (-)NCBI
Cytogenetic Map15q14NCBI
HuRef1511,385,680 - 11,493,609 (-)NCBIHuRef
CHM1_11534,640,225 - 34,748,321 (-)NCBICHM1_1
Slc12a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392112,096,659 - 112,193,508 (+)NCBIGRCm39mm39
GRCm39 Ensembl2112,096,170 - 112,193,508 (+)Ensembl
GRCm382112,266,314 - 112,363,163 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2112,265,825 - 112,363,163 (+)EnsemblGRCm38mm10GRCm38
MGSCv372112,106,471 - 112,203,320 (+)NCBIGRCm37mm9NCBIm37
MGSCv362112,067,658 - 112,163,995 (+)NCBImm8
Celera2113,423,625 - 113,514,137 (+)NCBICelera
Cytogenetic Map2E3NCBI
Slc12a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955416276,987 - 375,812 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955416277,215 - 375,812 (+)NCBIChiLan1.0ChiLan1.0
SLC12A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11531,575,336 - 31,681,016 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1531,576,756 - 31,680,061 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01512,741,526 - 12,846,894 (-)NCBIMhudiblu_PPA_v0panPan3
SLC12A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.130773,021 - 860,936 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl30773,933 - 858,487 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha30817,004 - 905,364 (+)NCBI
ROS_Cfam_1.030868,821 - 957,072 (+)NCBI
UMICH_Zoey_3.130817,202 - 905,323 (+)NCBI
UNSW_CanFamBas_1.030916,172 - 1,004,333 (+)NCBI
UU_Cfam_GSD_1.0301,043,815 - 1,131,948 (+)NCBI
Slc12a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864079,326,666 - 79,419,750 (+)NCBI
SpeTri2.0NW_0049366732,731,454 - 2,825,179 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC12A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl780,161,495 - 80,268,323 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1780,164,788 - 80,266,335 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SLC12A6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12648,570,399 - 48,673,935 (+)NCBI
ChlSab1.1 Ensembl2648,589,770 - 48,674,486 (+)Ensembl
Slc12a6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480431,489 - 105,944 (+)NCBI

Position Markers
BE114428  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2399,073,491 - 99,073,660 (+)MAPPER
Rnor_6.03103,754,513 - 103,754,681NCBIRnor6.0
Rnor_5.03110,349,375 - 110,349,543UniSTSRnor5.0
RGSC_v3.4398,111,822 - 98,111,990UniSTSRGSC3.4
Celera398,059,280 - 98,059,448UniSTS
RH 3.4 Map3873.7UniSTS
Cytogenetic Map3q34UniSTS
RH127577  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2399,169,847 - 99,170,047 (+)MAPPER
Rnor_6.03103,852,276 - 103,852,475NCBIRnor6.0
Rnor_5.03110,446,117 - 110,446,316UniSTSRnor5.0
RGSC_v3.4398,211,832 - 98,212,031UniSTSRGSC3.4
Celera398,155,325 - 98,155,524UniSTS
RH 3.4 Map3873.71UniSTS
Cytogenetic Map3q34UniSTS
RH129702  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2399,075,159 - 99,075,368 (+)MAPPER
Rnor_6.03103,756,340 - 103,756,547NCBIRnor6.0
Rnor_6.03103,756,181 - 103,756,547NCBIRnor6.0
Rnor_5.03110,351,202 - 110,351,409UniSTSRnor5.0
Rnor_5.03110,351,043 - 110,351,409UniSTSRnor5.0
RGSC_v3.4398,113,490 - 98,113,698UniSTSRGSC3.4
Celera398,060,948 - 98,061,156UniSTS
RH 3.4 Map3781.9UniSTS
Cytogenetic Map3q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333477354108914061Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)343295930108914061Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)354630948119830094Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)366711607119830094Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)366711607119830094Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)383817637119509260Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1582252Sual1Serum uric acid level QTL 13.40.0123blood uric acid amount (VT:0010302)blood uric acid level (CMO:0000501)3100730984106900596Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3100730984119830094Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:366
Count of miRNA genes:202
Interacting mature miRNAs:272
Transcripts:ENSRNOT00000007144
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 12 19 72 33 40 11
Low 43 45 41 41 8 11 2 2 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007144   ⟹   ENSRNOP00000007144
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3103,753,238 - 103,852,686 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079727   ⟹   ENSRNOP00000073931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3103,773,459 - 103,850,232 (+)Ensembl
RefSeq Acc Id: NM_001109630   ⟹   NP_001103100
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2399,072,217 - 99,170,258 (+)NCBI
Rnor_6.03103,753,238 - 103,852,686 (+)NCBI
Rnor_5.03110,347,112 - 110,446,527 (+)NCBI
RGSC_v3.4398,110,547 - 98,212,242 (+)RGD
Celera398,058,005 - 98,155,735 (+)RGD
Sequence:
RefSeq Acc Id: XM_006234710   ⟹   XP_006234772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2399,071,577 - 99,170,266 (+)NCBI
Rnor_6.03103,752,213 - 103,851,347 (+)NCBI
Rnor_5.03110,347,112 - 110,446,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006234711   ⟹   XP_006234773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2399,088,461 - 99,170,266 (+)NCBI
Rnor_6.03103,769,684 - 103,851,347 (+)NCBI
Rnor_5.03110,347,112 - 110,446,527 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001103100   ⟸   NM_001109630
- UniProtKB: G3V6N7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234772   ⟸   XM_006234710
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006234773   ⟸   XM_006234711
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K6T0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073931   ⟸   ENSRNOT00000079727
RefSeq Acc Id: ENSRNOP00000007144   ⟸   ENSRNOT00000007144
Protein Domains
AA_permease   SLC12

Transcriptome

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

Promoters
RGD ID:13692293
Promoter ID:EPDNEW_R2814
Type:initiation region
Name:Slc12a6_1
Description:solute carrier family 12, member 6
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_6.03103,773,543 - 103,773,603EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 98198242 98198243 G T snv HCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311335 AgrOrtholog
Ensembl Genes ENSRNOG00000005196 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007144 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073931 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007144 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079727 UniProtKB/TrEMBL
InterPro AA-permease_dom UniProtKB/TrEMBL
  K/Cl_cotranspt_1/3 UniProtKB/TrEMBL
  KCC1 UniProtKB/TrEMBL
  KCC3 UniProtKB/TrEMBL
  KCL_cotranspt UniProtKB/TrEMBL
  Na/K/Cl_cotransptS UniProtKB/TrEMBL
KEGG Report rno:691209 UniProtKB/TrEMBL
NCBI Gene 691209 ENTREZGENE
PANTHER PTHR11827:SF66 UniProtKB/TrEMBL
Pfam AA_permease UniProtKB/TrEMBL
  KCl_Cotrans_1 UniProtKB/TrEMBL
PhenoGen Slc12a6 PhenoGen
PRINTS KCLTRNSPORT UniProtKB/TrEMBL
  KCLTRNSPORT1 UniProtKB/TrEMBL
TIGRFAMs 2a30 UniProtKB/TrEMBL
UniProt A0A0G2K6T0 ENTREZGENE, UniProtKB/TrEMBL
  G3V6N7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-21 Slc12a6  solute carrier family 12, member 6  LOC691209  similar to Solute carrier family 12 member 6 (Electroneutral potassium-chloride cotransporter 3) (K-Cl cotransporter 3)  Data Merged 737654 APPROVED
2008-01-09 Slc12a6  solute carrier family 12, member 6  LOC687625  region containing solute carrier family 12, member 6; similar to K-Cl cotransporter 3a  Data Merged 1643240 APPROVED
2006-11-19 LOC687625  region containing solute carrier family 12, member 6; similar to K-Cl cotransporter 3a      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691209  similar to Solute carrier family 12 member 6 (Electroneutral potassium-chloride cotransporter 3) (K-Cl cotransporter 3)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Slc12a6  solute carrier family 12, member 6  Slc12a6_predicted  solute carrier family 12, member 6 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Slc12a6_predicted  solute carrier family 12, member 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED