Slc22a5 (solute carrier family 22 member 5) - Rat Genome Database

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Gene: Slc22a5 (solute carrier family 22 member 5) Rattus norvegicus
Analyze
Symbol: Slc22a5
Name: solute carrier family 22 member 5
RGD ID: 3702
Description: Enables (R)-carnitine transmembrane transporter activity. Involved in (R)-carnitine transmembrane transport. Located in basolateral plasma membrane and cytosol. Human ortholog(s) of this gene implicated in Crohn's disease; cardiomyopathy; inherited metabolic disorder; and systemic primary carnitine deficiency disease. Orthologous to human SLC22A5 (solute carrier family 22 member 5); INTERACTS WITH (+)-schisandrin B; (R)-carnitine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CT1; high-affinity carnitine transporter; high-affinity sodium-dependent carnitine cotransporter; integral membrane transport protein; OCTN2; organic cation/carnitine transporter; organic cation/carnitine transporter 2; solute carrier family 22 (organic cation transporter) member 5; solute carrier family 22 (organic cation transporter), member 5; solute carrier family 22 (organic cation/carnitine transporter), member 5; solute carrier family 22, member 5; UST2r
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21038,008,303 - 38,035,474 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1038,008,311 - 38,035,309 (-)Ensembl
Rnor_6.01039,201,101 - 39,228,090 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1039,201,107 - 39,323,853 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01038,982,882 - 39,009,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41039,311,729 - 39,338,718 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11039,325,353 - 39,352,341 (-)NCBI
Celera1037,351,299 - 37,378,255 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(R)-carnitine  (EXP,ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
allopurinol  (EXP,ISO)
amiodarone  (ISO)
angelicin  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
CAR(3:0(Me2))  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
cefaloridine  (EXP)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clozapine  (ISO)
Cuprizon  (EXP)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
cyproheptadine  (ISO)
decabromodiphenyl ether  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dichloroacetic acid  (ISO)
diphenhydramine  (ISO)
dithioerythritol  (EXP)
doxorubicin  (EXP,ISO)
dronedarone  (ISO)
Ebastine  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fructose  (EXP)
gemfibrozil  (EXP)
genistein  (ISO)
glafenine  (EXP)
glycine betaine  (ISO)
graphite  (EXP)
Grepafloxacin  (ISO)
hydroxyurea  (ISO)
ifosfamide  (EXP)
imperatorin  (ISO)
ipratropium  (ISO)
isoimperatorin  (ISO)
L-cysteine  (EXP)
leflunomide  (EXP)
lidocaine  (ISO)
mangiferin  (ISO)
meldonium  (EXP,ISO)
mepyramine  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
methoxsalen  (ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nifedipine  (ISO)
ofloxacin  (EXP,ISO)
olanzapine  (ISO)
omeprazole  (EXP)
oxycodone  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
Potassium 2,6-dihydroxytriazinecarboxylate  (ISO)
pravastatin  (EXP,ISO)
probenecid  (ISO)
progesterone  (ISO)
promethazine  (ISO)
propiconazole  (ISO)
propranolol  (ISO)
psoralen  (ISO)
quercetin  (EXP,ISO)
quetiapine fumarate  (ISO)
raloxifene  (ISO)
rotenone  (EXP)
spironolactone  (ISO)
sunitinib  (ISO)
talinolol  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
Tesaglitazar  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetraethylammonium  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
trans-piceid  (ISO)
trichloroethene  (ISO)
troglitazone  (EXP,ISO)
tunicamycin  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
verapamil  (ISO)
vorinostat  (ISO)
zaragozic acid A  (EXP,ISO)
zidovudine  (ISO)
ziprasidone  (ISO)

References

References - curated
1. Czeredys M, etal., PLoS One. 2013 Dec 13;8(12):e82105. doi: 10.1371/journal.pone.0082105. eCollection 2013.
2. Friedrich A, etal., Brain Res. 2003 Apr 4;968(1):69-79.
3. Ganapathy ME, etal., J Biol Chem. 2000 Jan 21;275(3):1699-707.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Jurkiewicz D, etal., Biochim Biophys Acta Mol Cell Res. 2017 May;1864(5):797-805. doi: 10.1016/j.bbamcr.2017.02.014. Epub 2017 Feb 28.
7. Karlic H, etal., J Mol Med. 2003 Jul;81(7):435-42. Epub 2003 Jun 12.
8. Kobayashi D, etal., Reproduction. 2005 Dec;130(6):931-7.
9. Kobayashi D, etal., Reproduction. 2005 Jun;129(6):729-36.
10. Maeda T, etal., Mol Pharm. 2007 Jul-Aug;4(4):600-7. Epub 2007 Jul 7.
11. Matsuishi T, etal., Neuropediatrics. 1985 Feb;16(1):6-12.
12. Melegh B, etal., Am J Med Genet A. 2004 Dec 1;131(2):121-6.
13. MGD data from the GO Consortium
14. Miecz D, etal., J Neurochem. 2008 Jan;104(1):113-23. doi: 10.1111/j.1471-4159.2007.05024.x. Epub 2007 Nov 6.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. OMIM Disease Annotation Pipeline
17. Peltekova VD, etal., Nat Genet. 2004 May;36(5):471-5. Epub 2004 Apr 11.
18. Rahbeeni Z, etal., J Inherit Metab Dis. 2002 Sep;25(5):363-9.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Rodriguez CM, etal., Biol Reprod. 2002 Jul;67(1):314-9.
23. Schomig E, etal., FEBS Lett 1998 Mar 20;425(1):79-86.
24. Sekine T, etal., Biochem Biophys Res Commun 1998 Oct 20;251(2):586-91.
25. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
26. Wu X, etal., J Pharmacol Exp Ther 1999 Sep;290(3):1482-92.
Additional References at PubMed
PMID:1996978   PMID:7773507   PMID:7914432   PMID:8155735   PMID:8325377   PMID:8670273   PMID:9140816   PMID:9618255   PMID:9634010   PMID:9685390   PMID:9916797   PMID:10087008  
PMID:10100867   PMID:10498652   PMID:11010964   PMID:12477932   PMID:15238359   PMID:15240869   PMID:15523054   PMID:17011512   PMID:17027329   PMID:17065219   PMID:17274673   PMID:17644405  
PMID:18005709   PMID:18408886   PMID:18520060   PMID:18641280   PMID:18762717   PMID:19056867   PMID:19150623   PMID:19684012   PMID:20112288   PMID:20143157   PMID:20219053   PMID:20381822  
PMID:22014179   PMID:22310714   PMID:22900493   PMID:28666211  


Genomics

Candidate Gene Status
Slc22a5 is a candidate Gene for QTL Eau7
Comparative Map Data
Slc22a5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21038,008,303 - 38,035,474 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1038,008,311 - 38,035,309 (-)Ensembl
Rnor_6.01039,201,101 - 39,228,090 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1039,201,107 - 39,323,853 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01038,982,882 - 39,009,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41039,311,729 - 39,338,718 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11039,325,353 - 39,352,341 (-)NCBI
Celera1037,351,299 - 37,378,255 (-)NCBICelera
Cytogenetic Map10q22NCBI
SLC22A5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5132,369,710 - 132,395,613 (+)EnsemblGRCh38hg38GRCh38
GRCh385132,369,704 - 132,395,614 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375131,705,402 - 131,731,304 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365131,733,343 - 131,759,205 (+)NCBINCBI36hg18NCBI36
Build 345131,733,342 - 131,759,202NCBI
Celera5127,835,468 - 127,861,380 (+)NCBI
Cytogenetic Map5q31.1NCBI
HuRef5126,897,648 - 126,923,551 (+)NCBIHuRef
CHM1_15131,138,142 - 131,164,051 (+)NCBICHM1_1
Slc22a5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,755,368 - 53,782,609 (-)NCBIGRCm39mm39
GRCm39 Ensembl1153,755,368 - 53,782,486 (-)Ensembl
GRCm381153,864,542 - 53,891,796 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1153,864,542 - 53,891,660 (-)EnsemblGRCm38mm10GRCm38
MGSCv371153,678,044 - 53,705,205 (-)NCBIGRCm37mm9NCBIm37
MGSCv361153,707,965 - 53,735,083 (-)NCBImm8
Celera1158,444,145 - 58,471,434 (-)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1132.02NCBI
SLC22A5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15133,954,549 - 133,980,410 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5133,954,678 - 133,979,066 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05127,791,984 - 127,817,870 (+)NCBIMhudiblu_PPA_v0panPan3
SLC22A5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11120,659,023 - 20,686,359 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1120,598,888 - 20,683,087 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1119,460,877 - 19,488,092 (+)NCBI
ROS_Cfam_1.01121,444,805 - 21,472,095 (+)NCBI
UMICH_Zoey_3.11120,163,703 - 20,190,915 (+)NCBI
UNSW_CanFamBas_1.01120,011,714 - 20,038,930 (+)NCBI
UU_Cfam_GSD_1.01120,653,571 - 20,680,804 (+)NCBI
Slc22a5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213115,771,008 - 115,795,734 (-)NCBI
SpeTri2.0NW_0049366472,774,063 - 2,798,585 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC22A5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12134,660,741 - 134,847,575 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22140,064,363 - 140,150,841 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC22A5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12335,197,909 - 35,224,466 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2335,197,985 - 35,223,137 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603442,719,642 - 42,746,187 (-)NCBIVero_WHO_p1.0
Slc22a5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473339,690,958 - 39,727,503 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131079  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21038,009,158 - 38,009,353 (+)MAPPERmRatBN7.2
mRatBN7.21038,104,987 - 38,105,182 (+)MAPPERmRatBN7.2
Rnor_6.01039,297,778 - 39,297,972NCBIRnor6.0
Rnor_6.01039,201,955 - 39,202,149NCBIRnor6.0
Rnor_5.01039,079,559 - 39,079,753UniSTSRnor5.0
Rnor_5.01038,983,736 - 38,983,930UniSTSRnor5.0
RGSC_v3.41039,312,583 - 39,312,777UniSTSRGSC3.4
RGSC_v3.41039,408,406 - 39,408,600UniSTSRGSC3.4
Celera1037,447,966 - 37,448,160UniSTS
Celera1037,352,153 - 37,352,347UniSTS
RH 3.4 Map10406.1UniSTS
Cytogenetic Map10q22UniSTS
AU047818  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21038,021,835 - 38,022,054 (+)MAPPERmRatBN7.2
Rnor_6.01039,214,632 - 39,214,850NCBIRnor6.0
Rnor_5.01038,996,413 - 38,996,631UniSTSRnor5.0
RGSC_v3.41039,325,260 - 39,325,478UniSTSRGSC3.4
RGSC_v3.41039,421,587 - 39,421,789UniSTSRGSC3.4
Celera1037,459,707 - 37,459,909UniSTS
Cytogenetic Map10q22UniSTS
RH137025  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21038,008,342 - 38,008,503 (+)MAPPERmRatBN7.2
Rnor_6.01039,201,139 - 39,201,299NCBIRnor6.0
Rnor_5.01038,982,920 - 38,983,080UniSTSRnor5.0
RGSC_v3.41039,311,767 - 39,311,927UniSTSRGSC3.4
Celera1037,351,337 - 37,351,497UniSTS
RH 3.4 Map10406.09UniSTS
Cytogenetic Map10q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:381
Count of miRNA genes:219
Interacting mature miRNAs:269
Transcripts:ENSRNOT00000011340
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.


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 1 2 2 1 2 25 19 1
Low 2 43 55 39 18 39 8 11 74 10 22 10 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005489780 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB017260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC120085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC135771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF110416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ001933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC166421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011340   ⟹   ENSRNOP00000011340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1038,008,311 - 38,035,296 (-)Ensembl
Rnor_6.0 Ensembl1039,201,107 - 39,228,090 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000041253   ⟹   ENSRNOP00000049867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1039,296,912 - 39,323,853 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081898   ⟹   ENSRNOP00000069462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1039,201,107 - 39,323,816 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086644   ⟹   ENSRNOP00000070765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1038,008,311 - 38,035,309 (-)Ensembl
Rnor_6.0 Ensembl1039,201,107 - 39,228,103 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104473   ⟹   ENSRNOP00000089083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1038,030,755 - 38,035,300 (-)Ensembl
RefSeq Acc Id: NM_019269   ⟹   NP_062142
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,305 - 38,035,296 (-)NCBI
Rnor_6.01039,201,101 - 39,228,090 (-)NCBI
Rnor_5.01038,982,882 - 39,009,871 (-)NCBI
RGSC_v3.41039,311,729 - 39,338,718 (-)RGD
Celera1037,351,299 - 37,378,255 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085791   ⟹   XP_038941719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,013,155 - 38,035,474 (-)NCBI
RefSeq Acc Id: XM_039085792   ⟹   XP_038941720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,015,173 - 38,035,473 (-)NCBI
RefSeq Acc Id: XM_039085793   ⟹   XP_038941721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,303 - 38,019,650 (-)NCBI
RefSeq Acc Id: XM_039085794   ⟹   XP_038941722
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,303 - 38,019,656 (-)NCBI
RefSeq Acc Id: XM_039085795   ⟹   XP_038941723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,303 - 38,027,571 (-)NCBI
RefSeq Acc Id: XR_005489777
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,308 - 38,035,474 (-)NCBI
RefSeq Acc Id: XR_005489778
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,013,206 - 38,035,474 (-)NCBI
RefSeq Acc Id: XR_005489779
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,015,173 - 38,035,474 (-)NCBI
RefSeq Acc Id: XR_005489780
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21038,008,308 - 38,035,474 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_062142   ⟸   NM_019269
- UniProtKB: O70594 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000049867   ⟸   ENSRNOT00000041253
RefSeq Acc Id: ENSRNOP00000069462   ⟸   ENSRNOT00000081898
RefSeq Acc Id: ENSRNOP00000011340   ⟸   ENSRNOT00000011340
RefSeq Acc Id: ENSRNOP00000070765   ⟸   ENSRNOT00000086644
RefSeq Acc Id: XP_038941723   ⟸   XM_039085795
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941722   ⟸   XM_039085794
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941721   ⟸   XM_039085793
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941719   ⟸   XM_039085791
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941720   ⟸   XM_039085792
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000089083   ⟸   ENSRNOT00000104473
Protein Domains
MFS

Transcriptome

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

Promoters
RGD ID:13697186
Promoter ID:EPDNEW_R7708
Type:initiation region
Name:Slc22a5_1
Description:solute carrier family 22 member 5
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_6.01039,228,136 - 39,228,196EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 38993070 38993071 C G snv F344/Jcl (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 39212469 39212470 T G snv BN/SsN (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 39323097 39323098 T G snv BN/SsN (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), LCR/2Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), HCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3702 AgrOrtholog
Ensembl Genes ENSRNOG00000008432 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011340 UniProtKB/Swiss-Prot
  ENSRNOP00000049867 UniProtKB/TrEMBL
  ENSRNOP00000069462 UniProtKB/TrEMBL
  ENSRNOP00000070765 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011340 UniProtKB/Swiss-Prot
  ENSRNOT00000041253 UniProtKB/TrEMBL
  ENSRNOT00000081898 UniProtKB/TrEMBL
  ENSRNOT00000086644 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9089728 IMAGE-MGC_LOAD
InterPro MFS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_sugar_transport-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Orgcat_transp/SVOP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sugar_transporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29726 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187372 IMAGE-MGC_LOAD
NCBI Gene 29726 ENTREZGENE
Pfam Sugar_tr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SLC22A5 RGD
PhenoGen Slc22a5 PhenoGen
PROSITE MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUGAR_TRANSPORT_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC218794
TIGRFAMs 2A0119 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JVF2_RAT UniProtKB/TrEMBL
  B2GUV4_RAT UniProtKB/TrEMBL
  O70594 ENTREZGENE
  Q3I408_RAT UniProtKB/TrEMBL
  S22A5_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LZE4 UniProtKB/TrEMBL
  Q9QWL0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc22a5  solute carrier family 22 member 5  Slc22a5  solute carrier family 22 (organic cation/carnitine transporter), member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-19 Slc22a5  solute carrier family 22 (organic cation/carnitine transporter), member 5  Slc22a5  solute carrier family 22 (organic cation transporter), member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc22a5  solute carrier family 22 (organic cation transporter), member 5    solute carrier family 22, member 5   Name updated 1299863 APPROVED
2002-06-10 Slc22a5  solute carrier family 22, member 5       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in kidney, heart, placenta and brain 70011
gene_function transports organic cations in the absence of sodium; transports carnitine in the presence of sodium 70011
gene_function transports organic cations in the absence of sodium; transports carnitine in the presence of sodium 730132
gene_mutations_overexpression human homolog mutant forms M352R and P478L are associated with a loss of transport activity 70011
gene_protein protein is 557 amino acids with 12 putative transmembrane domains 730132