Slc10a1 (solute carrier family 10 member 1) - Rat Genome Database
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Gene: Slc10a1 (solute carrier family 10 member 1) Rattus norvegicus
Analyze
Symbol: Slc10a1
Name: solute carrier family 10 member 1
RGD ID: 3681
Description: Exhibits bile acid:sodium symporter activity. Involved in several processes, including bile acid and bile salt transport; bile acid signaling pathway; and response to 17alpha-ethynylestradiol. Localizes to basolateral plasma membrane. Biomarker of alcoholic hepatitis; cholestasis; and obesity. Orthologous to human SLC10A1 (solute carrier family 10 member 1); PARTICIPATES IN bile acid signaling pathway; bile acid transport pathway; INTERACTS WITH (+)-schisandrin B; (-)-epigallocatechin 3-gallate; 1-benzylpiperazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Na(+)/bile acid cotransporter; Na(+)/taurocholate transport protein; NA-dependent cholate transporting protein; Ntcp; Ntcp1; SBACT; sodium-dependent bile acid cotransporter; sodium-dependent taurocholate cotransporting polypeptide; sodium/bile acid cotransporter; sodium/taurocholate cotransporting polypeptide; solute carrier family 10 (sodium/bile acid cotransporter family) member 1; Solute carrier family 10 (sodium/bile acid cotransporter family), member 1; solute carrier family 10 (sodium/bile acid cotransporter), member 1; solute carrier family 10, member 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
mRatBN7.26100,613,045 - 100,626,670 (-)NCBI
Rnor_6.0 Ensembl6104,617,730 - 104,631,355 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06104,617,730 - 104,631,355 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06112,782,934 - 112,796,559 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46104,735,839 - 104,749,464 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16104,739,294 - 104,752,920 (-)NCBI
Celera698,468,708 - 98,482,340 (-)NCBICelera
Cytogenetic Map6q24NCBI
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
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-benzylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
8-(4-chlorophenylthio)-cAMP  (ISO)
acadesine  (EXP)
acetamide  (EXP)
acetamides  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
allyl alcohol  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
atazanavir sulfate  (ISO)
atorvastatin calcium  (ISO)
azathioprine  (EXP)
aztreonam  (ISO)
benzenesulfonates  (ISO)
benzo[a]pyrene  (ISO)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bosentan  (EXP,ISO)
bromosulfophthalein  (ISO)
buta-1,3-diene  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
cefalotin  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlorpromazine  (EXP)
cholic acid  (ISO)
chrysophanol  (EXP)
ciprofibrate  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cocaine  (ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
cyproconazole  (ISO)
daidzein  (ISO)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
deoxycholic acid  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dichlorine  (EXP)
dieldrin  (EXP,ISO)
dihydroartemisinin  (EXP)
dioscin  (EXP)
doxycycline  (EXP)
emodin  (EXP,ISO)
endosulfan  (ISO)
enilconazole  (ISO)
epoxiconazole  (ISO)
estrone 3-sulfate  (ISO)
ethanol  (EXP,ISO)
fenofibrate  (EXP,ISO)
fipronil  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
fusidic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
Geniposide  (EXP)
genistein  (EXP)
ginsenoside Rg1  (EXP)
glafenine  (EXP)
glyburide  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
guggulsterone  (EXP,ISO)
GW 4064  (EXP,ISO)
Heliotrine  (ISO)
heptachlor  (EXP,ISO)
ibuprofen  (ISO)
imipenem hydrate  (ISO)
indole-3-acetic acid  (ISO)
indoxyl sulfate  (ISO)
isoniazide  (EXP)
ketoconazole  (EXP)
lead diacetate  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
macitentan  (ISO)
manganese(II) chloride  (EXP)
methamphetamine  (ISO)
methapyrilene  (EXP)
methotrexate  (EXP)
methoxsalen  (EXP)
methoxychlor  (EXP)
microcystin-LR  (ISO)
mirex  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-benzoylglycine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP,ISO)
neomycin  (ISO)
nimesulide  (EXP)
O-methyleugenol  (ISO)
obeticholic acid  (EXP,ISO)
oleanolic acid  (ISO)
oltipraz  (ISO)
ozone  (EXP)
paracetamol  (ISO)
perfluorobutanesulfonic acid  (EXP,ISO)
perfluorodecanoic acid  (ISO)
perfluorohexanesulfonic acid  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
perhexiline  (EXP)
phenobarbital  (EXP,ISO)
physcion  (EXP)
piperazines  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pravastatin  (EXP,ISO)
propiconazole  (ISO)
pyrazinecarboxamide  (EXP)
pyrrolidines  (EXP)
rifampicin  (ISO)
ritonavir  (ISO)
Ro 41-5253  (ISO)
senecionine  (EXP,ISO)
Senkirkine  (ISO)
serpentine asbestos  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium chloride  (ISO)
sodium dichromate  (EXP)
sulfoglycolithocholic acid  (ISO)
tamoxifen  (EXP,ISO)
taurocholic acid  (EXP,ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP,ISO)
thioacetamide  (EXP)
ticlopidine  (EXP)
Tolvaptan  (ISO)
trichloroethene  (ISO)
Triptolide  (ISO)
troglitazone  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
Yangonin  (ISO)
zaragozic acid A  (EXP,ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8662994   PMID:11279518   PMID:12477932   PMID:12547402   PMID:12631271   PMID:12842829   PMID:12883478   PMID:14684617   PMID:14701722   PMID:14711893   PMID:15361361   PMID:16027164  
PMID:16608845   PMID:17615179   PMID:17640976   PMID:17916651   PMID:19815625   PMID:20539008   PMID:21167233   PMID:23125159   PMID:24008362   PMID:25305012   PMID:26306036   PMID:27133208  
PMID:31088037  


Genomics

Comparative Map Data
Slc10a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26100,613,045 - 100,626,670 (-)NCBI
Rnor_6.0 Ensembl6104,617,730 - 104,631,355 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06104,617,730 - 104,631,355 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06112,782,934 - 112,796,559 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46104,735,839 - 104,749,464 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16104,739,294 - 104,752,920 (-)NCBI
Celera698,468,708 - 98,482,340 (-)NCBICelera
Cytogenetic Map6q24NCBI
SLC10A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1469,775,416 - 69,797,241 (-)EnsemblGRCh38hg38GRCh38
GRCh381469,775,416 - 69,797,241 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371470,242,133 - 70,263,958 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361469,312,305 - 69,333,707 (-)NCBINCBI36hg18NCBI36
Build 341469,312,304 - 69,333,707NCBI
Celera1450,306,664 - 50,328,118 (-)NCBI
Cytogenetic Map14q24.1NCBI
HuRef1450,411,110 - 50,432,563 (-)NCBIHuRef
CHM1_11470,180,694 - 70,202,147 (-)NCBICHM1_1
Slc10a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391280,999,959 - 81,015,479 (-)NCBIGRCm39mm39
GRCm39 Ensembl1280,999,957 - 81,015,479 (-)Ensembl
GRCm381280,953,185 - 80,968,705 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1280,953,183 - 80,968,705 (-)EnsemblGRCm38mm10GRCm38
MGSCv371282,054,172 - 82,069,066 (-)NCBIGRCm37mm9NCBIm37
MGSCv361281,874,340 - 81,886,832 (-)NCBImm8
Celera1282,418,707 - 82,433,538 (-)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1237.21NCBI
Slc10a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955466597,204 - 608,756 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955466597,081 - 609,254 (+)NCBIChiLan1.0ChiLan1.0
SLC10A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11469,240,602 - 69,261,904 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1469,240,602 - 69,261,904 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01450,369,663 - 50,390,984 (-)NCBIMhudiblu_PPA_v0panPan3
SLC10A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl843,521,747 - 43,546,274 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1843,521,291 - 43,546,426 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc10a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649512,958,983 - 12,975,755 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC10A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl793,397,602 - 93,421,985 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1793,400,037 - 93,421,989 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2799,679,201 - 99,699,835 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC10A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12447,018,237 - 47,034,360 (-)NCBI
ChlSab1.1 Ensembl2447,017,414 - 47,033,940 (-)Ensembl
Slc10a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473431,287,539 - 31,307,339 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000007825
Prediction methods:Miranda
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 32 29 4 29 3 2
Low 3 10 25 12 15 12 8 9 11 19 5 9 8
Below cutoff 3 2 8 10 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007825   ⟹   ENSRNOP00000007825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6104,617,730 - 104,631,355 (-)Ensembl
RefSeq Acc Id: NM_017047   ⟹   NP_058743
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,613,045 - 100,626,670 (-)NCBI
Rnor_6.06104,617,730 - 104,631,355 (-)NCBI
Rnor_5.06112,782,934 - 112,796,559 (-)NCBI
RGSC_v3.46104,735,839 - 104,749,464 (-)RGD
Celera698,468,708 - 98,482,340 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058743   ⟸   NM_017047
- UniProtKB: P26435 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007825   ⟸   ENSRNOT00000007825

Transcriptome

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

Promoters
RGD ID:13694702
Promoter ID:EPDNEW_R5227
Type:initiation region
Name:Slc10a1_1
Description:solute carrier family 10 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_6.06104,631,310 - 104,631,370EPDNEW

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


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 104630941 104630942 G C snv SR/JrHsd (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3681 AgrOrtholog
Ensembl Genes ENSRNOG00000005794 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007825 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007825 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1530.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7370832 IMAGE-MGC_LOAD
InterPro BilAc:Na_symport/Acr3 UniProtKB/Swiss-Prot
  Bilac:Na_transpt UniProtKB/Swiss-Prot
  Na+/solute_symporter_sf UniProtKB/Swiss-Prot
  SLC10A1 UniProtKB/Swiss-Prot
KEGG Report rno:24777 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108711 IMAGE-MGC_LOAD
NCBI Gene 24777 ENTREZGENE
PANTHER PTHR10361 UniProtKB/Swiss-Prot
  PTHR10361:SF40 UniProtKB/Swiss-Prot
Pfam SBF UniProtKB/Swiss-Prot
PharmGKB SLC10A1 RGD
PhenoGen Slc10a1 PhenoGen
TIGRFAMs bass UniProtKB/Swiss-Prot
UniProt NTCP_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5BK99 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc10a1  solute carrier family 10 member 1  Slc10a1  solute carrier family 10 (sodium/bile acid cotransporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc10a1  solute carrier family 10 (sodium/bile acid cotransporter family), member 1    solute carrier family 10, member 1  Name updated 1299863 APPROVED
2003-04-09 Slc10a1  solute carrier family 10, member 1    Solute carrier family 10 (sodium/bile acid cotransporter family), member 1  Name updated 629478 APPROVED
2002-06-10 Slc10a1  Solute carrier family 10 (sodium/bile acid cotransporter family), member 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression reduced in response to certain types of liver damage 70249
gene_regulation transporter activity is induced by cAMP via phosphoinositide 3-kinase/protein kinase B mediated signaling 727378