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

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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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85136,660,022 - 136,694,173 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5136,659,948 - 136,694,172 (+)EnsemblGRCr8
mRatBN7.25131,374,562 - 131,408,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,374,542 - 131,408,728 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5134,079,676 - 134,113,767 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05135,834,289 - 135,868,384 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05135,856,719 - 135,890,810 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,669,674 - 136,703,702 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,669,674 - 136,703,697 (+)Ensemblrn6Rnor6.0
Rnor_5.05140,458,723 - 140,492,751 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45138,300,869 - 138,334,893 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5129,922,904 - 129,957,106 (+)NCBICelera
RGSC_v3.15138,313,795 - 138,339,599 (+)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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)
okadaic acid  (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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5136,659,948 - 136,694,172 (+)EnsemblGRCr8
mRatBN7.25131,374,562 - 131,408,733 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,374,542 - 131,408,728 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5134,079,676 - 134,113,767 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05135,834,289 - 135,868,384 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05135,856,719 - 135,890,810 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,669,674 - 136,703,702 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,669,674 - 136,703,697 (+)Ensemblrn6Rnor6.0
Rnor_5.05140,458,723 - 140,492,751 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45138,300,869 - 138,334,893 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5129,922,904 - 129,957,106 (+)NCBICelera
RGSC_v3.15138,313,795 - 138,339,599 (+)NCBI
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 (-)Ensemblhg38GRCh38
GRCh37144,462,155 - 44,497,134 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36144,234,742 - 44,269,721 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm384117,835,258 - 117,869,305 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4117,834,506 - 117,875,198 (+)Ensemblmm10GRCm38
MGSCv374117,507,863 - 117,541,910 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1516,356,708 - 16,389,086 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01516,390,376 - 16,422,650 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248923,275,034 - 3,308,579 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Slc6a9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1139,152,247 - 39,172,357 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Slc6a9
280 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5102105698152749382Rat
2303586Gluco52Glucose level QTL 522blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)5100826632145826632Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
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)5116702075161702075Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5130678987145274255Rat
7365049Bp359Blood pressure QTL 359arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133308734140009902Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134369218156289444Rat
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)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)592583776137583776Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112142946157142946Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112142946157142946Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5110770739155770739Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
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)551657967166600247Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112142946157142946Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)592583776137583776Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)598972960143972960Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)592583776137583776Rat
2303618Vencon1Ventilatory control QTL 13.8respiration trait (VT:0001943)oxygen consumption (CMO:0002169)5100826632145826632Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111236572156236572Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)594034903139034903Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114131300159131300Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125969677156302135Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)560601597137492949Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112142946157142946Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112142946157142946Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116702075161702075Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)574335621156302135Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116702075161702075Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114131300159131300Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)592881678137881678Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5104262817153890625Rat

Markers in Region
D5Mit14  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85136,663,521 - 136,663,694 (+)Marker Load Pipeline
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
Celera5129,926,365 - 129,926,537UniSTS
RGSC_v3.15138,309,475 - 138,309,647RGD
RH 3.4 Map5860.5UniSTS
RH 3.4 Map5860.5RGD
RH 2.0 Map5849.6RGD
Cytogenetic Map5q36UniSTS
D5Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85136,677,460 - 136,677,614 (+)Marker Load Pipeline
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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 85 59 6 349 185 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000048770   ⟹   ENSRNOP00000040252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5136,659,948 - 136,694,172 (+)Ensembl
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
GRCr8 Ensembl5136,674,045 - 136,694,170 (+)Ensembl
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, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000048770 ENTREZGENE
  ENSRNOT00000085527 ENTREZGENE
  ENSRNOT00000085527.2 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:8364347 IMAGE-MGC_LOAD
InterPro Na/ntran_symport UniProtKB/Swiss-Prot
  Na/ntran_symport_glycine_GLY1 UniProtKB/Swiss-Prot
  SNS_sf UniProtKB/Swiss-Prot
KEGG Report rno:116509 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156610 IMAGE-MGC_LOAD
NCBI Gene 116509 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot
  SODIUM- AND CHLORIDE-DEPENDENT GLYCINE TRANSPORTER 1 UniProtKB/Swiss-Prot
Pfam SNF UniProtKB/Swiss-Prot
PhenoGen Slc6a9 PhenoGen
PRINTS GLY1TRNSPORT UniProtKB/Swiss-Prot
  NANEUSMPORT UniProtKB/Swiss-Prot
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000019484 RatGTEx
Superfamily-SCOP SSF161070 UniProtKB/Swiss-Prot
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