Slc1a6 (solute carrier family 1 member 6) - Rat Genome Database

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Gene: Slc1a6 (solute carrier family 1 member 6) Rattus norvegicus
Analyze
Symbol: Slc1a6
Name: solute carrier family 1 member 6
RGD ID: 620340
Description: Enables high-affinity L-glutamate transmembrane transporter activity and monoatomic anion transmembrane transporter activity. Involved in L-glutamate import across plasma membrane. Located in plasma membrane. Part of membrane protein complex. Is active in parallel fiber to Purkinje cell synapse and postsynaptic membrane. Orthologous to human SLC1A6 (solute carrier family 1 member 6); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EAAT4; excitatory amino acid transporter 4; high affinity aspartate/glutamate transporter; high-affinity neuronal glutamate transporter; MGC114297; sodium-dependent glutamate/aspartate transporter; solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8711,492,422 - 11,521,007 (-)NCBIGRCr8
mRatBN7.2710,841,836 - 10,870,424 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,841,837 - 10,870,449 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx713,661,837 - 13,690,559 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0715,539,283 - 15,568,001 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,417,320 - 13,445,815 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0713,730,101 - 13,758,170 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl713,730,253 - 13,751,271 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,893,841 - 13,921,839 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,393,284 - 12,419,893 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1712,393,284 - 12,419,880 (-)NCBI
Celera78,958,917 - 8,988,056 (-)NCBICelera
Cytogenetic Map7q11NCBI
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
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Caveolin-1 Sensitivity of Excitatory Amino Acid Transporters EAAT1, EAAT2, EAAT3, and EAAT4. Abousaab A, etal., J Membr Biol. 2016 Jun;249(3):239-49. doi: 10.1007/s00232-015-9863-0. Epub 2015 Dec 21.
2. Similar perisynaptic glial localization for the Na+,K+-ATPase alpha 2 subunit and the glutamate transporters GLAST and GLT-1 in the rat somatosensory cortex. Cholet N, etal., Cereb Cortex 2002 May;12(5):515-25.
3. The glutamate transporter EAAT4 in rat cerebellar Purkinje cells: a glutamate-gated chloride channel concentrated near the synapse in parts of the dendritic membrane facing astroglia. Dehnes Y, etal., J Neurosci. 1998 May 15;18(10):3606-19.
4. Glutamate transporter protein subtypes are expressed differentially during rat CNS development. Furuta A, etal., J Neurosci. 1997 Nov 1;17(21):8363-75.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7791878   PMID:12477932   PMID:14506254   PMID:14715943   PMID:14727177   PMID:16601148   PMID:16837599   PMID:17490622   PMID:18540911   PMID:18770868   PMID:19747495   PMID:20110679  
PMID:20231455   PMID:21070388   PMID:21127051   PMID:21572047   PMID:21700703   PMID:23049999   PMID:29476059  


Genomics

Comparative Map Data
Slc1a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8711,492,422 - 11,521,007 (-)NCBIGRCr8
mRatBN7.2710,841,836 - 10,870,424 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,841,837 - 10,870,449 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx713,661,837 - 13,690,559 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0715,539,283 - 15,568,001 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,417,320 - 13,445,815 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0713,730,101 - 13,758,170 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl713,730,253 - 13,751,271 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,893,841 - 13,921,839 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,393,284 - 12,419,893 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1712,393,284 - 12,419,880 (-)NCBI
Celera78,958,917 - 8,988,056 (-)NCBICelera
Cytogenetic Map7q11NCBI
SLC1A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381914,950,033 - 15,010,643 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1914,950,033 - 15,022,990 (-)EnsemblGRCh38hg38GRCh38
GRCh371915,060,845 - 15,121,455 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361914,921,991 - 14,944,730 (-)NCBINCBI36Build 36hg18NCBI36
Build 341914,921,990 - 14,944,730NCBI
Celera1914,956,703 - 14,979,425 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1914,628,668 - 14,688,622 (-)NCBIHuRef
CHM1_11915,060,322 - 15,120,899 (-)NCBICHM1_1
T2T-CHM13v2.01915,074,841 - 15,135,544 (-)NCBIT2T-CHM13v2.0
Slc1a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391078,615,923 - 78,650,659 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1078,616,330 - 78,650,599 (+)EnsemblGRCm39 Ensembl
GRCm381078,780,086 - 78,814,825 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1078,780,496 - 78,814,765 (+)EnsemblGRCm38mm10GRCm38
MGSCv371078,243,241 - 78,277,570 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361078,183,631 - 78,217,894 (+)NCBIMGSCv36mm8
Celera1079,802,330 - 79,836,572 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Slc1a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554958,289,734 - 8,314,874 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554958,270,601 - 8,314,874 (+)NCBIChiLan1.0ChiLan1.0
SLC1A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22019,865,671 - 19,896,124 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11918,882,684 - 18,913,146 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01914,499,333 - 14,529,781 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11915,470,222 - 15,498,980 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1915,470,222 - 15,526,471 (-)Ensemblpanpan1.1panPan2
SLC1A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12047,133,237 - 47,143,512 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2047,097,593 - 47,143,512 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2046,976,526 - 46,993,225 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02047,618,429 - 47,635,339 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2047,589,356 - 47,635,118 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12046,849,336 - 46,866,041 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02047,267,243 - 47,284,105 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02047,539,683 - 47,556,398 (+)NCBIUU_Cfam_GSD_1.0
Slc1a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118205,914,191 - 205,929,855 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365965,464,862 - 5,478,641 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365965,464,850 - 5,478,763 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC1A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl262,601,758 - 62,623,371 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1262,601,763 - 62,623,597 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2262,160,514 - 62,181,952 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC1A6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1613,537,902 - 13,567,333 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl613,538,064 - 13,558,959 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660746,023,993 - 6,056,899 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc1a6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249012,017,381 - 2,048,282 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249012,021,097 - 2,048,456 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc1a6
221 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:120
Interacting mature miRNAs:128
Transcripts:ENSRNOT00000009931
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat


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 30
Low 7 7 7 42 6 29 3
Below cutoff 1 14 32 24 6 24 2 2 2 10 12 6 2

Sequence


RefSeq Acc Id: ENSRNOT00000009931   ⟹   ENSRNOP00000009931
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,841,837 - 10,870,449 (-)Ensembl
Rnor_6.0 Ensembl713,730,253 - 13,751,271 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108905   ⟹   ENSRNOP00000096116
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,841,837 - 10,870,449 (-)Ensembl
RefSeq Acc Id: NM_032065   ⟹   NP_114454
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8711,492,422 - 11,521,007 (-)NCBI
mRatBN7.2710,841,836 - 10,870,424 (-)NCBI
Rnor_6.0713,730,101 - 13,758,099 (-)NCBI
Rnor_5.0713,893,841 - 13,921,839 (-)NCBI
RGSC_v3.4712,393,284 - 12,419,893 (-)RGD
Celera78,958,917 - 8,988,056 (-)RGD
Sequence:
RefSeq Acc Id: NP_114454   ⟸   NM_032065
- UniProtKB: P97683 (UniProtKB/Swiss-Prot),   O35921 (UniProtKB/Swiss-Prot),   Q7TSX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009931   ⟸   ENSRNOT00000009931
RefSeq Acc Id: ENSRNOP00000096116   ⟸   ENSRNOT00000108905

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35921-F1-model_v2 AlphaFold O35921 1-561 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620340 AgrOrtholog
BioCyc Gene G2FUF-34849 BioCyc
Ensembl Genes ENSRNOG00000007509 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009931.6 UniProtKB/TrEMBL
  ENSRNOT00000108905 ENTREZGENE
  ENSRNOT00000108905.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.3860.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7315936 IMAGE-MGC_LOAD
InterPro Na-dicarboxylate_symporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na-dicarboxylate_symporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na:dicarbo_symporter_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84012 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:114297 IMAGE-MGC_LOAD
NCBI Gene 84012 ENTREZGENE
PANTHER EXCITATORY AMINO ACID TRANSPORTER 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM/DICARBOXYLATE SYMPORTER-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SDF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc1a6 PhenoGen
PRINTS EDTRNSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NA_DICARBOXYL_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_DICARBOXYL_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007509 RatGTEx
Superfamily-SCOP SSF118215 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6K924_RAT UniProtKB/TrEMBL
  EAA4_RAT UniProtKB/Swiss-Prot
  F1LR26_RAT UniProtKB/TrEMBL
  O35921 ENTREZGENE
  P97683 ENTREZGENE
  Q7TSX6 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P97683 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc1a6  solute carrier family 1 member 6  Slc1a6  solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc1a6  solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Slc1a6  solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6      Symbol and Name status set to provisional 70820 PROVISIONAL