Slc6a9 (solute carrier family 6 member 9) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Slc6a9 (solute carrier family 6 member 9) Rattus norvegicus
Analyze
Symbol: Slc6a9
Name: solute carrier family 6 member 9
RGD ID: 621243
Description: Enables glycine:sodium symporter activity. Involved in glycine import across plasma membrane. Located in dense core granule; endosome; and plasma membrane. Is active in several cellular components, including hippocampal mossy fiber to CA3 synapse; parallel fiber to Purkinje cell synapse; and synaptic membrane. Orthologous to human SLC6A9 (solute carrier family 6 member 9); INTERACTS WITH (+)-schisandrin B; 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: glycine transporter 1; glycine transporter variant 1a; GLYT-1; GLYT-1b; Glyt1; sodium- and chloride-dependent glycine transporter 1; solute carrier family 6 (neurotransmitter transporter, glycine), member 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85136,660,022 - 136,694,173 (+)NCBIGRCr8
mRatBN7.25131,374,562 - 131,408,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,374,542 - 131,408,728 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5134,079,676 - 134,113,767 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05135,834,289 - 135,868,384 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05135,856,719 - 135,890,810 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,669,674 - 136,703,702 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,669,674 - 136,703,697 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05140,458,723 - 140,492,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45138,300,869 - 138,334,893 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15138,313,795 - 138,339,599 (+)NCBI
Celera5129,922,904 - 129,957,106 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-butoxyethanol  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
amitrole  (EXP)
amphetamine  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzamide  (EXP)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
butan-1-ol  (ISO)
cadmium dichloride  (EXP,ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clodronic acid  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumarin  (EXP)
Cuprizon  (EXP)
cyclosporin A  (EXP,ISO)
DDE  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
diclofenac  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
enniatin  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP,ISO)
fenofibrate  (EXP,ISO)
fipronil  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glycine betaine  (EXP)
glyphosate  (EXP)
ibuprofen  (ISO)
ifosfamide  (ISO)
inulin  (ISO)
iron dichloride  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
mercury dichloride  (EXP)
metformin  (EXP)
methamphetamine  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N(4)-hydroxycytidine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
nobiletin  (EXP,ISO)
oxaliplatin  (EXP)
oxycodone  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP,ISO)
phorone  (EXP)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
pyrazinecarboxamide  (EXP)
rifampicin  (ISO)
rotenone  (EXP,ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
sevoflurane  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sotorasib  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trametinib  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (EXP)
trovafloxacin  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Two glycine transporter variants with distinct localization in the CNS and peripheral tissues are encoded by a common gene. Borowsky B, etal., Neuron 1993 May;10(5):851-63.
2. Localization of the GLYT1 glycine transporter at glutamatergic synapses in the rat brain. Cubelos B, etal., Cereb Cortex. 2005 Apr;15(4):448-59. doi: 10.1093/cercor/bhh147.
3. The scaffolding protein PSD-95 interacts with the glycine transporter GLYT1 and impairs its internalization. Cubelos B, etal., J Neurochem. 2005 Nov;95(4):1047-58.
4. Localization of the glycine transporter GLYT1 in glutamatergic synaptic vesicles. Cubelos B, etal., Neurochem Int. 2014 Jul;73:204-10. doi: 10.1016/j.neuint.2013.09.002. Epub 2013 Sep 11.
5. The glycine transporter GLYT1 interacts with Sec3, a component of the exocyst complex. Cubelos B, etal., Neuropharmacology. 2005 Nov;49(6):935-44. doi: 10.1016/j.neuropharm.2005.07.021. Epub 2005 Sep 21.
6. 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.
7. Glycine transporter isoforms show differential subcellular localization in PC12 cells. Geerlings A, etal., J Neurochem. 2002 Jul;82(1):58-65. doi: 10.1046/j.1471-4159.2002.00930.x.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Cloning, expression, and localization of a rat brain high-affinity glycine transporter. Guastella J, etal., Proc Natl Acad Sci U S A 1992 Aug 1;89(15):7189-93.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Cloning and expression of a glycine transporter reveal colocalization with NMDA receptors. Smith KE, etal., Neuron 1992 May;8(5):927-35.
Additional References at PubMed
PMID:1618338   PMID:9786914   PMID:10722844   PMID:12477932   PMID:12602503   PMID:16289893   PMID:17724084   PMID:17980459   PMID:18695510   PMID:18775105   PMID:18778746   PMID:18973561  
PMID:19473961   PMID:19666071   PMID:19711201   PMID:21574997   PMID:22871113   PMID:22988142   PMID:23529192   PMID:25057202   PMID:26200505   PMID:26302655   PMID:33484385  


Genomics

Comparative Map Data
Slc6a9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85136,660,022 - 136,694,173 (+)NCBIGRCr8
mRatBN7.25131,374,562 - 131,408,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,374,542 - 131,408,728 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5134,079,676 - 134,113,767 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05135,834,289 - 135,868,384 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05135,856,719 - 135,890,810 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,669,674 - 136,703,702 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,669,674 - 136,703,697 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05140,458,723 - 140,492,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45138,300,869 - 138,334,893 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15138,313,795 - 138,339,599 (+)NCBI
Celera5129,922,904 - 129,957,106 (+)NCBICelera
Cytogenetic Map5q36NCBI
SLC6A9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38143,996,483 - 44,031,462 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl143,991,500 - 44,031,467 (-)EnsemblGRCh38hg38GRCh38
GRCh37144,462,155 - 44,497,134 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,234,742 - 44,269,721 (-)NCBINCBI36Build 36hg18NCBI36
Build 34144,132,286 - 44,152,090NCBI
Celera142,745,693 - 42,780,672 (-)NCBICelera
Cytogenetic Map1p34.1NCBI
HuRef142,577,665 - 42,612,669 (-)NCBIHuRef
CHM1_1144,578,322 - 44,613,386 (-)NCBICHM1_1
T2T-CHM13v2.0143,859,929 - 43,902,553 (-)NCBIT2T-CHM13v2.0
Slc6a9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394117,692,240 - 117,726,502 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4117,691,703 - 117,732,395 (+)EnsemblGRCm39 Ensembl
GRCm384117,835,258 - 117,869,305 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4117,834,506 - 117,875,198 (+)EnsemblGRCm38mm10GRCm38
MGSCv374117,507,863 - 117,541,910 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364117,333,190 - 117,367,237 (+)NCBIMGSCv36mm8
Celera4116,550,328 - 116,584,414 (+)NCBICelera
Cytogenetic Map4D1NCBI
cM Map453.62NCBI
Slc6a9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555373,520,516 - 3,550,022 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555373,520,516 - 3,549,492 (-)NCBIChiLan1.0ChiLan1.0
SLC6A9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21182,778,098 - 182,813,151 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11181,919,460 - 181,954,476 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0143,298,326 - 43,333,345 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1144,669,364 - 44,704,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl144,664,839 - 44,704,882 (-)Ensemblpanpan1.1panPan2
SLC6A9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11516,235,342 - 16,267,161 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1516,235,482 - 16,267,933 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1516,356,708 - 16,389,086 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01516,390,376 - 16,422,650 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1516,390,493 - 16,422,543 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11516,189,225 - 16,221,582 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01516,257,816 - 16,290,585 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01516,330,949 - 16,363,315 (+)NCBIUU_Cfam_GSD_1.0
Slc6a9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505859,487,760 - 59,520,209 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647425,313,201 - 25,345,053 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647425,312,544 - 25,344,993 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6167,268,963 - 167,301,599 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16167,267,193 - 167,301,598 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26154,781,274 - 154,783,428 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12088,774,354 - 88,809,726 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2088,774,339 - 88,808,669 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603328,117,914 - 28,153,448 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc6a9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248923,275,034 - 3,305,692 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248923,275,034 - 3,308,579 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc6a9
150 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:221
Count of miRNA genes:129
Interacting mature miRNAs:159
Transcripts:ENSRNOT00000048770
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
7365049Bp359Blood pressure QTL 359arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128071929134724733Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5128033842133011550Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat

Markers in Region
D5Mit14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,378,081 - 131,378,254 (+)MAPPERmRatBN7.2
Rnor_6.05136,673,054 - 136,673,226NCBIRnor6.0
Rnor_5.05140,462,103 - 140,462,275UniSTSRnor5.0
RGSC_v3.45138,304,248 - 138,304,421RGDRGSC3.4
RGSC_v3.45138,304,249 - 138,304,421UniSTSRGSC3.4
RGSC_v3.15138,309,475 - 138,309,647RGD
Celera5129,926,365 - 129,926,537UniSTS
RH 3.4 Map5860.5UniSTS
RH 3.4 Map5860.5RGD
RH 2.0 Map5849.6RGD
Cytogenetic Map5q36UniSTS
D5Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,392,020 - 131,392,174 (+)MAPPERmRatBN7.2
Rnor_6.05136,686,993 - 136,687,146NCBIRnor6.0
Rnor_5.05140,476,042 - 140,476,195UniSTSRnor5.0
RGSC_v3.45138,318,189 - 138,318,342UniSTSRGSC3.4
Celera5129,940,391 - 129,940,558UniSTS
Cytogenetic Map5q36UniSTS
RH143473  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,405,819 - 131,405,996 (+)MAPPERmRatBN7.2
Rnor_6.05136,700,789 - 136,700,965NCBIRnor6.0
Rnor_5.05140,489,838 - 140,490,014UniSTSRnor5.0
RGSC_v3.45138,331,985 - 138,332,161UniSTSRGSC3.4
Celera5129,954,204 - 129,954,380UniSTS
RH 3.4 Map5855.9UniSTS
Cytogenetic Map5q36UniSTS
RH141917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,408,476 - 131,408,656 (+)MAPPERmRatBN7.2
Rnor_6.05136,703,446 - 136,703,625NCBIRnor6.0
Rnor_5.05140,492,495 - 140,492,674UniSTSRnor5.0
RGSC_v3.45138,334,642 - 138,334,821UniSTSRGSC3.4
Celera5129,956,855 - 129,957,034UniSTS
RH 3.4 Map5860.8UniSTS
Cytogenetic Map5q36UniSTS
AA943440  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,399,543 - 131,399,735 (+)MAPPERmRatBN7.2
Rnor_6.05136,694,516 - 136,694,707NCBIRnor6.0
Rnor_5.05140,483,565 - 140,483,756UniSTSRnor5.0
RGSC_v3.45138,325,712 - 138,325,903UniSTSRGSC3.4
Celera5129,947,928 - 129,948,119UniSTS
RH 3.4 Map5858.2UniSTS
Cytogenetic Map5q36UniSTS
Glyt1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,408,382 - 131,408,588 (+)MAPPERmRatBN7.2
Rnor_6.05136,703,352 - 136,703,557NCBIRnor6.0
Rnor_5.05140,492,401 - 140,492,606UniSTSRnor5.0
RGSC_v3.45138,334,548 - 138,334,753UniSTSRGSC3.4
Celera5129,956,761 - 129,956,966UniSTS
Cytogenetic Map5q36UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000048770   ⟹   ENSRNOP00000040252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,374,542 - 131,408,728 (+)Ensembl
Rnor_6.0 Ensembl5136,669,674 - 136,703,697 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085527   ⟹   ENSRNOP00000070161
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,388,620 - 131,407,781 (+)Ensembl
Rnor_6.0 Ensembl5136,683,592 - 136,702,750 (+)Ensembl
RefSeq Acc Id: NM_053818   ⟹   NP_446270
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,660,076 - 136,694,173 (+)NCBI
mRatBN7.25131,374,636 - 131,408,733 (+)NCBI
Rnor_6.05136,669,674 - 136,703,697 (+)NCBI
Rnor_5.05140,458,723 - 140,492,751 (+)NCBI
RGSC_v3.45138,300,869 - 138,334,893 (+)RGD
Celera5129,922,904 - 129,957,106 (+)RGD
Sequence:
RefSeq Acc Id: XM_006238625   ⟹   XP_006238687
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,673,789 - 136,694,173 (+)NCBI
mRatBN7.25131,388,571 - 131,408,733 (+)NCBI
Rnor_6.05136,683,486 - 136,703,702 (+)NCBI
Rnor_5.05140,458,723 - 140,492,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109142   ⟹   XP_038965070
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,660,022 - 136,694,173 (+)NCBI
mRatBN7.25131,374,562 - 131,408,733 (+)NCBI
RefSeq Acc Id: XM_039109143   ⟹   XP_038965071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,674,020 - 136,694,173 (+)NCBI
mRatBN7.25131,388,582 - 131,408,733 (+)NCBI
RefSeq Acc Id: NP_446270   ⟸   NM_053818
- UniProtKB: A6JZE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238687   ⟸   XM_006238625
- Peptide Label: isoform X1
- UniProtKB: Q63322 (UniProtKB/Swiss-Prot),   A1A5N0 (UniProtKB/Swiss-Prot),   Q63323 (UniProtKB/Swiss-Prot),   P28572 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070161   ⟸   ENSRNOT00000085527
Ensembl Acc Id: ENSRNOP00000040252   ⟸   ENSRNOT00000048770
RefSeq Acc Id: XP_038965070   ⟸   XM_039109142
- Peptide Label: isoform X2
- UniProtKB: A0A8L2ULJ7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965071   ⟸   XM_039109143
- Peptide Label: isoform X2
- UniProtKB: A0A8L2ULJ7 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P28572-F1-model_v2 AlphaFold P28572 1-638 view protein structure

Transcriptome

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

Promoters
RGD ID:13693956
Promoter ID:EPDNEW_R4481
Type:initiation region
Name:Slc6a9_1
Description:solute carrier family 6 member 9
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_6.05136,669,707 - 136,669,767EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621243 AgrOrtholog
BioCyc Gene G2FUF-40186 BioCyc
Ensembl Genes ENSRNOG00000019484 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048770.4 UniProtKB/TrEMBL
  ENSRNOT00000085527.2 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8364347 IMAGE-MGC_LOAD
InterPro Na/ntran_symport UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/ntran_symport_glycine_GLY1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116509 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:156610 IMAGE-MGC_LOAD
NCBI Gene 116509 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM- AND CHLORIDE-DEPENDENT GLYCINE TRANSPORTER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc6a9 PhenoGen
PRINTS GLY1TRNSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NANEUSMPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019484 RatGTEx
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2ULJ7 ENTREZGENE, UniProtKB/TrEMBL
  A1A5N0 ENTREZGENE
  A6JZE5 ENTREZGENE, UniProtKB/TrEMBL
  P28572 ENTREZGENE
  Q63322 ENTREZGENE
  Q63323 ENTREZGENE
  SC6A9_RAT UniProtKB/Swiss-Prot
UniProt Secondary A1A5N0 UniProtKB/Swiss-Prot
  Q63322 UniProtKB/Swiss-Prot
  Q63323 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc6a9  solute carrier family 6 member 9  Slc6a9  solute carrier family 6 (neurotransmitter transporter, glycine), member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc6a9  solute carrier family 6 (neurotransmitter transporter, glycine), member 9  Glyt1  glycine transporter 1  Symbol and Name updated 1299863 APPROVED
2002-08-07 Glyt1  glycine transporter 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_drugs transport blocked by sarcosine but is not blocked by methyl-aminoisobutyric acid or L-alanine 632884
gene_protein 633 amino acids with a molecular mass of approximately 70 kDA 632884