Slc17a6 (solute carrier family 17 member 6) - Rat Genome Database
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Gene: Slc17a6 (solute carrier family 17 member 6) Rattus norvegicus
Analyze
Symbol: Slc17a6
Name: solute carrier family 17 member 6
RGD ID: 620531
Description: Exhibits L-glutamate transmembrane transporter activity. Involved in hippocampus development and neural retina development. Localizes to cytoplasmic vesicle; excitatory synapse; and pericellular basket. Biomarker of transient cerebral ischemia. Orthologous to human SLC17A6 (solute carrier family 17 member 6); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH (S)-nicotine; 2,3,7,8-Tetrachlorodibenzofuran; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: differentation-associated Na-dependent inorganic phosphate cotransporter; differentiation-associated BNPI; differentiation-associated Na(+)-dependent inorganic phosphate cotransporter; Dnpi; solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6; solute carrier family 17 (vesicular glutamate transporter), member 6; vesicular glutamate transporter 2; VGLUT2
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
mRatBN7.21101,212,489 - 101,252,543 (+)NCBI
Rnor_6.0 Ensembl1106,998,623 - 107,038,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01106,980,463 - 107,038,717 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01108,040,511 - 108,080,524 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41101,425,975 - 101,466,023 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11101,504,085 - 101,544,133 (+)NCBI
Celera195,386,910 - 95,426,949 (+)NCBICelera
Cytogenetic Map1q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Boulland JL, etal., Cereb Cortex. 2009 Jan;19(1):241-8. doi: 10.1093/cercor/bhn077. Epub 2008 May 22.
2. Boulland JL, etal., J Comp Neurol. 2004 Dec 13;480(3):264-80.
3. Fattorini G, etal., J Neurochem. 2009 Sep;110(5):1538-46. Epub 2009 Jul 15.
4. Fremeau RT, etal., Neuron. 2001 Aug 2;31(2):247-60.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Hayashi M, etal., J Biol Chem 2001 Nov 16;276(46):43400-6.
7. Hioki H, etal., Neuroscience 2003;117(1):1-6.
8. Hrabovszky E, etal., Endocrinology 2005 Jan;146(1):341-7. Epub 2004 Oct 14.
9. Li JL, etal., J Comp Neurol 2003 Aug 18;463(2):212-20.
10. Li JL, etal., J Comp Neurol 2003 Mar 10;457(3):236-49.
11. Liu YY, etal., Eur J Neurosci 2003 Jan;17(1):41-8.
12. Llorente IL, etal., Brain Res Bull. 2013 May;94:90-7. doi: 10.1016/j.brainresbull.2013.02.006. Epub 2013 Feb 28.
13. Martin-Ibanez R, etal., Eur J Neurosci. 2006 Feb;23(4):1063-70.
14. MGD data from the GO Consortium
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Pipeline to import KEGG annotations from KEGG into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Riedel A, etal., J Chem Neuroanat. 2008 Dec;36(3-4):177-90. doi: 10.1016/j.jchemneu.2008.06.003. Epub 2008 Jun 19.
21. Stella SL Jr, etal., Brain Res. 2008 Jun 18;1215:20-9. doi: 10.1016/j.brainres.2008.03.038. Epub 2008 Apr 1.
Additional References at PubMed
PMID:11432869   PMID:11698620   PMID:14667459   PMID:14677070   PMID:14681932   PMID:15009640   PMID:15028755   PMID:15065123   PMID:15205380   PMID:15224985   PMID:15305861   PMID:15379996  
PMID:15382259   PMID:15682395   PMID:15714284   PMID:15845085   PMID:15908131   PMID:15983996   PMID:16079394   PMID:16423326   PMID:16481069   PMID:16786558   PMID:16842872   PMID:17046815  
PMID:17175111   PMID:17299752   PMID:17337147   PMID:17825268   PMID:17826944   PMID:17965879   PMID:18291592   PMID:18358609   PMID:18381590   PMID:18436385   PMID:18973592   PMID:19058187  
PMID:19191347   PMID:19264112   PMID:19778580   PMID:19844994   PMID:20217347   PMID:20339872   PMID:20533365   PMID:20593358   PMID:21375596   PMID:21609737   PMID:21957077   PMID:21982845  
PMID:22570693   PMID:22871113   PMID:23047588   PMID:23326507   PMID:23380804   PMID:23543101   PMID:23835161   PMID:23897509   PMID:24308494   PMID:24639017   PMID:24906290   PMID:25290694  
PMID:26362885   PMID:27210824   PMID:29462701   PMID:29465786   PMID:29476059   PMID:29476240   PMID:29650024   PMID:32439795  


Genomics

Comparative Map Data
Slc17a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21101,212,489 - 101,252,543 (+)NCBI
Rnor_6.0 Ensembl1106,998,623 - 107,038,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01106,980,463 - 107,038,717 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01108,040,511 - 108,080,524 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41101,425,975 - 101,466,023 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11101,504,085 - 101,544,133 (+)NCBI
Celera195,386,910 - 95,426,949 (+)NCBICelera
Cytogenetic Map1q22NCBI
SLC17A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1122,338,381 - 22,379,503 (+)EnsemblGRCh38hg38GRCh38
GRCh381122,338,381 - 22,379,503 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371122,359,927 - 22,401,049 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371122,359,667 - 22,401,049 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361122,316,243 - 22,357,619 (+)NCBINCBI36hg18NCBI36
Build 341122,316,242 - 22,357,619NCBI
Celera1122,492,722 - 22,534,075 (+)NCBI
Cytogenetic Map11p14.3NCBI
HuRef1122,042,899 - 22,084,263 (+)NCBIHuRef
CHM1_11122,359,385 - 22,400,763 (+)NCBICHM1_1
Slc17a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39751,271,578 - 51,320,874 (+)NCBIGRCm39mm39
GRCm38751,621,830 - 51,671,126 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl751,622,006 - 51,671,119 (+)EnsemblGRCm38mm10GRCm38
MGSCv37758,877,200 - 58,926,496 (+)NCBIGRCm37mm9NCBIm37
MGSCv36751,490,086 - 51,539,138 (+)NCBImm8
Celera749,002,489 - 49,051,776 (+)NCBICelera
Cytogenetic Map7B4NCBI
Slc17a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554762,813,368 - 2,854,514 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554762,813,368 - 2,854,371 (+)NCBIChiLan1.0ChiLan1.0
SLC17A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11122,257,983 - 22,299,443 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1122,258,011 - 22,301,944 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01122,350,537 - 22,392,009 (+)NCBIMhudiblu_PPA_v0panPan3
SLC17A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2144,016,133 - 44,054,931 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12144,015,161 - 44,056,286 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc17a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366543,039,825 - 3,082,788 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC17A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl237,098,992 - 37,138,475 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1237,098,983 - 37,138,935 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2240,309,860 - 40,349,435 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC17A6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1142,634,754 - 42,677,309 (-)NCBI
ChlSab1.1 Ensembl142,636,512 - 42,677,165 (-)Ensembl
Slc17a6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476613,335,186 - 13,376,634 (+)NCBI

Position Markers
AI060126  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01107,038,421 - 107,038,606NCBIRnor6.0
Rnor_5.01108,080,228 - 108,080,413UniSTSRnor5.0
RGSC_v3.41101,465,740 - 101,465,925UniSTSRGSC3.4
Celera195,426,666 - 95,426,851UniSTS
RH 3.4 Map1944.1UniSTS
Cytogenetic Map1q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)191093646136093646Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)194225372130917265Rat
1300153Bp171Blood pressure QTL 1713.37arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)194364073153076991Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)199983293127203999Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100354344145354344Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:217
Count of miRNA genes:145
Interacting mature miRNAs:175
Transcripts:ENSRNOT00000022383
Prediction methods:Miranda, 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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 70
Low 4 3
Below cutoff 9 3 5 3 4 4 21 7 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022383   ⟹   ENSRNOP00000022383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1106,998,623 - 107,038,704 (+)Ensembl
RefSeq Acc Id: NM_053427   ⟹   NP_445879
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21101,212,489 - 101,252,543 (+)NCBI
Rnor_6.01106,998,704 - 107,038,704 (+)NCBI
Rnor_5.01108,040,511 - 108,080,524 (+)NCBI
RGSC_v3.41101,425,975 - 101,466,023 (+)RGD
Celera195,386,910 - 95,426,949 (+)RGD
Sequence:
RefSeq Acc Id: XM_006229265   ⟹   XP_006229327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01107,001,329 - 107,037,073 (+)NCBI
Rnor_5.01108,040,511 - 108,080,524 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589793   ⟹   XP_017445282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01106,980,480 - 107,038,717 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589794   ⟹   XP_017445283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01106,980,463 - 107,038,704 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_445879 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF76223 (Get FASTA)   NCBI Sequence Viewer  
  EDM07210 (Get FASTA)   NCBI Sequence Viewer  
  Q9JI12 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445879   ⟸   NM_053427
- UniProtKB: Q9JI12 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006229327   ⟸   XM_006229265
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017445283   ⟸   XM_017589794
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017445282   ⟸   XM_017589793
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000022383   ⟸   ENSRNOT00000022383
Protein Domains
MFS

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620531 AgrOrtholog
Ensembl Genes ENSRNOG00000016147 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022383 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022383 ENTREZGENE, UniProtKB/TrEMBL
InterPro MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84487 UniProtKB/Swiss-Prot
NCBI Gene 84487 ENTREZGENE
Pfam MFS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc17a6 PhenoGen
PROSITE MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V851_RAT UniProtKB/TrEMBL
  Q9JI12 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc17a6  solute carrier family 17 member 6  Slc17a6  solute carrier family 17 (vesicular glutamate transporter), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc17a6  solute carrier family 17 (vesicular glutamate transporter), member 6  Slc17a6  solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc17a6  solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6  Dnpi  differentation-associated Na-dependent inorganic phosphate cotransporter  Symbol and Name updated 1299863 APPROVED
2002-08-07 Dnpi  differentation-associated Na-dependent inorganic phosphate cotransporter      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localizes on early endosomes 628484
gene_expression mRNA expressed in the inferior olivary complex, most brainstem precerebellar nuclei sending mossy fibers, and in axon terminals of nociceptive primary afferent fibers 632573
gene_expression mRNA expressed in the inferior olivary complex, most brainstem precerebellar nuclei sending mossy fibers, and in axon terminals of nociceptive primary afferent fibers 632574
gene_expression present in neuronla cells,preferentially expressed in pinealocytes, pancreatic alpha cells, alpha cells of Langerhans islets, pancreatic polypeptide-secreting F cells of Langerhans islets 628484
gene_function transports L-glutamate involving an electrochemical gradient of protons generated by vacuolar proton pump; vesicular transporter in glutamatergic endocrine cells and neurons 628484
gene_function vesicular glutamate transporter 628484
gene_process responsible for vesicular storage of L-glutamate 628484
gene_process may be involved in a dominant excitatory synaptic pathway 632575