Slc38a1 (solute carrier family 38, member 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Slc38a1 (solute carrier family 38, member 1) Rattus norvegicus
Analyze
Symbol: Slc38a1
Name: solute carrier family 38, member 1
RGD ID: 69645
Description: Enables L-amino acid transmembrane transporter activity and neutral amino acid:sodium symporter activity. Involved in L-alpha-amino acid transmembrane transport; female pregnancy; and neutral amino acid transport. Located in external side of apical plasma membrane and neuronal cell body. Biomarker of visual epilepsy. Orthologous to human SLC38A1 (solute carrier family 38 member 1); PARTICIPATES IN glutamate signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; acetamide; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: amino acid transporter A1; amino acid transporter system A1; Ata1; GlnT; glutamine transporter; N-system amino acid transporter 2; rATA1; Sat1; sodium-coupled neutral amino acid transporter 1; solute carrier family 38 member 1; system A amino acid transporter 1; system A transporter 2; system N amino acid transporter 1
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
mRatBN7.27127,733,230 - 127,802,541 (-)NCBI
Rnor_6.0 Ensembl7137,975,549 - 138,039,984 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07137,970,555 - 138,040,098 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07137,598,311 - 137,667,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47135,252,257 - 135,316,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17135,328,704 - 135,392,693 (-)NCBI
Celera7124,242,806 - 124,306,590 (-)NCBICelera
Cytogenetic Map7q35NCBI
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
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
cadmium sulfate  (ISO)
calyculin a  (ISO)
cannabidiol  (ISO)
cannabigerol  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dieldrin  (EXP)
endosulfan  (EXP)
ethanol  (ISO)
fenvalerate  (EXP,ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gamma-aminobutyric acid  (EXP)
geldanamycin  (ISO)
graphite  (EXP)
heptachlor  (EXP)
hydrogen chloride  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mirex  (EXP)
N,N-diethyl-m-toluamide  (EXP)
nickel dichloride  (ISO)
oxaliplatin  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
progesterone  (EXP)
Pyridostigmine bromide  (EXP)
quercetin  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
temozolomide  (ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zearalenone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11325958   PMID:12477932   PMID:15521011   PMID:16023720   PMID:16200463   PMID:17323379   PMID:20458337   PMID:20492358   PMID:20602128   PMID:25957749   PMID:26590355  


Genomics

Comparative Map Data
Slc38a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27127,733,230 - 127,802,541 (-)NCBI
Rnor_6.0 Ensembl7137,975,549 - 138,039,984 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07137,970,555 - 138,040,098 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07137,598,311 - 137,667,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47135,252,257 - 135,316,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17135,328,704 - 135,392,693 (-)NCBI
Celera7124,242,806 - 124,306,590 (-)NCBICelera
Cytogenetic Map7q35NCBI
SLC38A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1246,183,063 - 46,270,017 (-)EnsemblGRCh38hg38GRCh38
GRCh381246,183,063 - 46,269,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371246,576,846 - 46,662,826 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361244,863,105 - 44,949,475 (-)NCBINCBI36hg18NCBI36
Build 341244,867,850 - 44,948,816NCBI
Celera1245,374,176 - 45,460,544 (-)NCBI
Cytogenetic Map12q13.11NCBI
HuRef1243,608,096 - 43,694,464 (-)NCBIHuRef
CHM1_11246,541,943 - 46,628,310 (-)NCBICHM1_1
Slc38a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391596,469,299 - 96,541,396 (-)NCBIGRCm39mm39
GRCm39 Ensembl1596,469,299 - 96,540,794 (-)Ensembl
GRCm381596,571,418 - 96,643,438 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1596,571,418 - 96,642,913 (-)EnsemblGRCm38mm10GRCm38
MGSCv371596,401,849 - 96,473,344 (-)NCBIGRCm37mm9NCBIm37
MGSCv361596,402,709 - 96,452,131 (-)NCBImm8
Celera1598,716,978 - 98,788,897 (-)NCBICelera
Cytogenetic Map15F1NCBI
Slc38a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555005,398,358 - 5,462,042 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555005,393,211 - 5,468,827 (-)NCBIChiLan1.0ChiLan1.0
SLC38A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11243,333,087 - 43,419,502 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1243,362,597 - 43,413,616 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01242,464,360 - 42,550,324 (+)NCBIMhudiblu_PPA_v0panPan3
SLC38A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1278,110,327 - 8,179,394 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl278,130,823 - 8,174,936 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2738,127,750 - 38,197,361 (-)NCBI
ROS_Cfam_1.0278,309,904 - 8,379,147 (+)NCBI
UMICH_Zoey_3.1278,117,874 - 8,187,129 (+)NCBI
UNSW_CanFamBas_1.0278,156,867 - 8,221,929 (+)NCBI
UU_Cfam_GSD_1.02738,367,553 - 38,436,859 (-)NCBI
Slc38a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494568,660,514 - 68,726,003 (+)NCBI
SpeTri2.0NW_0049365124,438,827 - 4,504,416 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC38A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1577,009,840 - 77,076,723 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2579,935,364 - 80,001,646 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC38A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11142,415,986 - 42,502,794 (-)NCBI
ChlSab1.1 Ensembl1142,421,910 - 42,472,838 (-)Ensembl
Vero_WHO_p1.0NW_023666037203,924,850 - 204,006,548 (+)NCBI
Slc38a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248165,988,625 - 6,025,987 (+)NCBI

Position Markers
RH130789  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27127,803,358 - 127,803,530 (+)MAPPER
Rnor_6.07138,040,771 - 138,040,942NCBIRnor6.0
Rnor_5.07137,668,527 - 137,668,698UniSTSRnor5.0
RGSC_v3.47135,317,397 - 135,317,568UniSTSRGSC3.4
Celera7124,307,731 - 124,307,902UniSTS
RH 3.4 Map71092.0UniSTS
Cytogenetic Map7q35UniSTS
RH131580  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27127,737,986 - 127,738,171 (+)MAPPER
Rnor_6.07137,975,310 - 137,975,494NCBIRnor6.0
Rnor_5.07137,603,066 - 137,603,250UniSTSRnor5.0
RGSC_v3.47135,252,026 - 135,252,210UniSTSRGSC3.4
Celera7124,242,575 - 124,242,759UniSTS
RH 3.4 Map71092.0UniSTS
Cytogenetic Map7q35UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:53
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000008138
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 30 14 19 14 1 1 74 23 41 3 1
Low 1 21 21 21 7 10 12 8 7
Below cutoff 6 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008138   ⟹   ENSRNOP00000008138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7137,975,549 - 138,039,630 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089806   ⟹   ENSRNOP00000070624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7137,975,772 - 138,039,984 (-)Ensembl
RefSeq Acc Id: NM_138832   ⟹   NP_620187
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27127,738,218 - 127,802,218 (-)NCBI
Rnor_6.07137,975,541 - 138,039,630 (-)NCBI
Rnor_5.07137,598,311 - 137,667,871 (-)NCBI
RGSC_v3.47135,252,257 - 135,316,256 (-)RGD
Celera7124,242,806 - 124,306,590 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242277   ⟹   XP_006242339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27127,733,230 - 127,800,819 (-)NCBI
Rnor_6.07137,970,555 - 138,039,326 (-)NCBI
Rnor_5.07137,598,311 - 137,667,871 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242280   ⟹   XP_006242342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27127,733,230 - 127,802,169 (-)NCBI
Rnor_6.07137,970,555 - 138,039,731 (-)NCBI
Rnor_5.07137,598,311 - 137,667,871 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242281   ⟹   XP_006242343
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27127,733,230 - 127,802,541 (-)NCBI
Rnor_6.07137,970,555 - 138,040,098 (-)NCBI
Rnor_5.07137,598,311 - 137,667,871 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078321   ⟹   XP_038934249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27127,733,230 - 127,758,622 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_620187   ⟸   NM_138832
- UniProtKB: Q9JM15 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242343   ⟸   XM_006242281
- Peptide Label: isoform X1
- UniProtKB: Q9JM15 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242342   ⟸   XM_006242280
- Peptide Label: isoform X1
- UniProtKB: Q9JM15 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242339   ⟸   XM_006242277
- Peptide Label: isoform X1
- UniProtKB: Q9JM15 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008138   ⟸   ENSRNOT00000008138
RefSeq Acc Id: ENSRNOP00000070624   ⟸   ENSRNOT00000089806
RefSeq Acc Id: XP_038934249   ⟸   XM_039078321
- Peptide Label: isoform X2

Transcriptome

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

Promoters
RGD ID:13695608
Promoter ID:EPDNEW_R6133
Type:initiation region
Name:Slc38a1_1
Description:solute carrier family 38, member 1
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_6.07138,039,687 - 138,039,747EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69645 AgrOrtholog
Ensembl Genes ENSRNOG00000005291 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000008138 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070624 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000008138 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000089806 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7444889 IMAGE-MGC_LOAD
InterPro AA_transpt_TM UniProtKB/Swiss-Prot
KEGG Report rno:170567 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114262 IMAGE-MGC_LOAD
NCBI Gene 170567 ENTREZGENE
Pfam Aa_trans UniProtKB/Swiss-Prot
PhenoGen Slc38a1 PhenoGen
TIGR TC232025
UniProt Q9JM15 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Slc38a1  solute carrier family 38, member 1      Symbol and Name status set to approved 70586 APPROVED
2002-02-27 Slc38a1  solute carrier family 38, member 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70292 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localizes to somata and proximal dendrites 1299220
gene_function transports glutamine from glutamatergic neurons 68922
gene_process supplies glutamatergic neurons with serine and cysteine 68922
gene_process may have a role in providing metabolic fuel (via alpha-ketoglutarate) or precursors for glutathione synthesis 1299220