Slc11a2 (solute carrier family 11 member 2) - Rat Genome Database

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Gene: Slc11a2 (solute carrier family 11 member 2) Rattus norvegicus
Analyze
Symbol: Slc11a2
Name: solute carrier family 11 member 2
RGD ID: 3684
Description: Enables lead ion transmembrane transporter activity; transition metal ion binding activity; and transition metal ion transmembrane transporter activity. Involved in several processes, including cellular response to tumor necrosis factor; response to lead ion; and transition metal ion transport. Located in apical part of cell; late endosome membrane; and lysosomal membrane. Is integral component of membrane. Used to study Parkinsonism; hypochromic anemia; and pneumonia. Biomarker of brain ischemia; duodenal ulcer; and iron deficiency anemia. Human ortholog(s) of this gene implicated in Parkinson's disease; amyotrophic lateral sclerosis; anemia; and hypochromic anemia. Orthologous to human SLC11A2 (solute carrier family 11 member 2); PARTICIPATES IN hypoxia inducible factor pathway; iron uptake pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: divalent cation transporter 1; divalent metal transporter 1; DMT-1; DMT1; natural resistance-associated macrophage protein 2; NRAMP 2; Nramp2; solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2; solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2; Solute carrier family 11 member 2 (natural resistance-associated macrophage protein 2)
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
mRatBN7.27131,503,076 - 131,540,246 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7131,503,081 - 131,540,145 (-)Ensembl
Rnor_6.07142,025,812 - 142,062,892 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,025,815 - 142,063,212 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,833,529 - 139,870,819 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,094,505 - 139,127,427 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17139,170,941 - 139,203,864 (-)NCBI
Celera7127,985,198 - 128,017,825 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-methylcholine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
alcohol  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
astragaloside IV  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
captan  (ISO)
chlorogenic acid  (EXP)
chromium(6+)  (EXP,ISO)
clobetasol  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
deferiprone  (ISO)
Deguelin  (ISO)
desferrioxamine B  (EXP,ISO)
dibutyl phthalate  (EXP)
diltiazem  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
divanadium pentaoxide  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP)
ebselen  (ISO)
elemental selenium  (ISO)
erastin  (EXP)
ethanol  (ISO)
ferric ammonium citrate  (ISO)
flutamide  (EXP)
folpet  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
glucose  (ISO)
hydrogen peroxide  (ISO)
iron atom  (EXP,ISO)
iron dextran  (ISO)
iron trichloride  (ISO)
iron(0)  (EXP,ISO)
iron(2+) sulfate (anhydrous)  (ISO)
iron(III) nitrilotriacetate  (ISO)
isobutanol  (ISO)
isotretinoin  (ISO)
kainic acid  (EXP)
L-ascorbic acid  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (ISO)
Methylazoxymethanol acetate  (EXP)
methylmercury chloride  (ISO)
mithramycin  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
nimodipine  (ISO)
nitric oxide  (EXP,ISO)
nitroprusside  (ISO)
ochratoxin A  (EXP,ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
quercetin  (EXP,ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (EXP,ISO)
sodium dichromate  (EXP,ISO)
staurosporine  (ISO)
succimer  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
titanium dioxide  (EXP)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
uranium atom  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vanadium atom  (EXP)
vanadium dioxide  (ISO)
vanadium(0)  (EXP)
verapamil  (ISO)
vitamin E  (ISO)
Yessotoxin  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (ISO)
zinc oxide  (ISO)
zinc sulfate  (ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Abouhamed M, etal., Am J Physiol Renal Physiol. 2006 Jun;290(6):F1525-33. Epub 2006 Jan 31.
2. Beaumont C, etal., Blood. 2006 May 15;107(10):4168-70. Epub 2006 Jan 26.
3. Blasco H, etal., J Neurol Sci. 2011 Apr 15;303(1-2):124-7. Epub 2011 Jan 26.
4. Catoire H, etal., Ann Neurol. 2011 Jul;70(1):170-5. doi: 10.1002/ana.22435. Epub 2011 Jun 27.
5. Dzikaite V, etal., J Hepatol. 2006 Mar;44(3):544-51. Epub 2005 Aug 22.
6. Ferguson CJ, etal., Am J Physiol Renal Physiol 2001 May;280(5):F803-14.
7. Fleming MD, etal., Nat Genet. 1997 Aug;16(4):383-6.
8. Fleming MD, etal., Proc Natl Acad Sci U S A 1998 Feb 3;95(3):1148-53.
9. Garcia SJ, etal., Toxicol Sci. 2007 Jan;95(1):205-14. Epub 2006 Oct 23.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Gu C, etal., Neurochem Res. 2009 Jun;34(6):1150-6. Epub 2008 Dec 14.
13. Gunshin H, etal., Nature 1997 Jul 31;388(6641):482-8.
14. He Q, etal., Neurosci Lett. 2011 Sep 1;501(3):128-31. Epub 2011 Jul 12.
15. Jiang H, etal., Cell Res. 2010 Mar;20(3):345-56. Epub 2010 Feb 2.
16. Khomenko T, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Jun;296(6):G1277-86. doi: 10.1152/ajpgi.90257.2008. Epub 2009 Apr 2.
17. Kim J, etal., Am J Physiol Lung Cell Mol Physiol. 2011 Apr;300(4):L659-65. Epub 2011 Jan 28.
18. Lane DJ, etal., Biochim Biophys Acta. 2015 May;1853(5):1130-44. doi: 10.1016/j.bbamcr.2015.01.021. Epub 2015 Feb 4.
19. Leong WI, etal., Am J Physiol Gastrointest Liver Physiol 2003 Dec;285(6):G1153-61. Epub 2003 Sep 04.
20. Mackenzie B, etal., Pflugers Arch. 2006 Jan;451(4):544-58. Epub 2005 Aug 10.
21. MGD data from the GO Consortium
22. Mims MP, etal., Blood. 2005 Feb 1;105(3):1337-42. Epub 2004 Sep 30.
23. Monnot AD, etal., Exp Biol Med (Maywood). 2012 Mar;237(3):327-33. doi: 10.1258/ebm.2011.011170.
24. Moos T and Morgan EH, J Neurochem. 2004 Jan;88(1):233-45.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. Salazar J, etal., Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18578-83. Epub 2008 Nov 14.
31. Simovich MJ, etal., Am J Hematol 2002 Mar;69(3):164-70.
32. Song N, etal., J Neurosci Res. 2007 Nov 1;85(14):3118-26.
33. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
34. Thompson K, etal., FASEB J. 2007 Jan;21(1):223-30. Epub 2006 Nov 20.
35. Wang X, etal., Exp Biol Med (Maywood). 2008 Dec;233(12):1561-71. Epub 2008 Oct 10.
36. Wang X, etal., Toxicol Appl Pharmacol. 2008 Jul 15;230(2):167-74. Epub 2008 Mar 6.
37. Wang XS, etal., Exp Neurol 2002 Sep;177(1):193-201.
38. Wareing M, etal., Am J Physiol Renal Physiol. 2003 Dec;285(6):F1050-9. Epub 2003 Jul 22.
39. Xiong L, etal., Am J Med Genet B Neuropsychiatr Genet. 2007 Oct 5;144B(7):911-7.
40. Yang F, etal., Biometals. 2010 Aug;23(4):657-67. Epub 2010 Mar 25.
41. Yang L, etal., Cell Physiol Biochem. 2011;27(1):23-30. Epub 2011 Feb 11.
Additional References at PubMed
PMID:658175   PMID:807277   PMID:4404581   PMID:5070129   PMID:10751401   PMID:10942769   PMID:11090085   PMID:11739192   PMID:11842004   PMID:12127992   PMID:12209011   PMID:12475959  
PMID:12477932   PMID:12522007   PMID:12662899   PMID:12724326   PMID:12734107   PMID:12767048   PMID:12949888   PMID:14531808   PMID:15019308   PMID:15024413   PMID:15355847   PMID:15660380  
PMID:15736955   PMID:15792797   PMID:15849611   PMID:15880641   PMID:15908475   PMID:15994289   PMID:16075245   PMID:16142913   PMID:16227996   PMID:16539692   PMID:16879716   PMID:16905747  
PMID:17097837   PMID:17109629   PMID:17293870   PMID:17596526   PMID:17640977   PMID:17897319   PMID:17932044   PMID:18076961   PMID:18082289   PMID:18189270   PMID:18191877   PMID:18375546  
PMID:18419598   PMID:18776082   PMID:19211831   PMID:19240805   PMID:19252488   PMID:19655216   PMID:19946888   PMID:20007457   PMID:20164305   PMID:22154351   PMID:22465424   PMID:22871113  
PMID:23349308   PMID:23361852   PMID:23447582   PMID:23506423   PMID:24239078   PMID:24318355   PMID:24448823   PMID:24850829   PMID:25115800   PMID:25318588   PMID:25326704   PMID:25491917  
PMID:25501899   PMID:25745840   PMID:26078704   PMID:26360295   PMID:26506412   PMID:26617777   PMID:27331785   PMID:27462458   PMID:28669019   PMID:29317744  


Genomics

Comparative Map Data
Slc11a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27131,503,076 - 131,540,246 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7131,503,081 - 131,540,145 (-)Ensembl
Rnor_6.07142,025,812 - 142,062,892 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,025,815 - 142,063,212 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,833,529 - 139,870,819 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,094,505 - 139,127,427 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17139,170,941 - 139,203,864 (-)NCBI
Celera7127,985,198 - 128,017,825 (-)NCBICelera
Cytogenetic Map7q36NCBI
SLC11A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1250,979,401 - 51,028,566 (-)EnsemblGRCh38hg38GRCh38
GRCh381250,952,263 - 51,028,886 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371251,373,190 - 51,422,669 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361249,666,044 - 49,706,409 (-)NCBINCBI36hg18NCBI36
Build 341249,666,043 - 49,706,409NCBI
Celera1250,175,791 - 50,224,278 (-)NCBI
Cytogenetic Map12q13.12NCBI
HuRef1248,405,542 - 48,453,948 (-)NCBIHuRef
CHM1_11251,339,878 - 51,388,358 (-)NCBICHM1_1
Slc11a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915100,285,779 - 100,322,090 (-)NCBIGRCm39mm39
GRCm39 Ensembl15100,285,779 - 100,322,953 (-)Ensembl
GRCm3815100,387,898 - 100,424,209 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15100,387,898 - 100,425,072 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715100,218,329 - 100,253,486 (-)NCBIGRCm37mm9NCBIm37
MGSCv3615100,215,932 - 100,251,017 (-)NCBImm8
Celera15102,539,003 - 102,574,160 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1556.29NCBI
SLC11A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11238,629,576 - 38,677,377 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1238,629,686 - 38,677,377 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01237,726,158 - 37,774,554 (+)NCBIMhudiblu_PPA_v0panPan3
SLC11A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,788,785 - 3,823,852 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,787,855 - 3,822,672 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2742,433,184 - 42,468,214 (-)NCBI
ROS_Cfam_1.0273,835,730 - 3,870,717 (+)NCBI
UMICH_Zoey_3.1273,802,428 - 3,837,405 (+)NCBI
UNSW_CanFamBas_1.0273,789,782 - 3,824,709 (+)NCBI
UU_Cfam_GSD_1.02742,829,654 - 42,864,682 (-)NCBI
Slc11a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494564,541,218 - 64,575,407 (+)NCBI
SpeTri2.0NW_0049365128,590,302 - 8,622,121 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC11A2
(Sus scrofa - pig)
No map positions available.
SLC11A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11147,190,138 - 47,238,543 (-)NCBI
ChlSab1.1 Ensembl1147,197,168 - 47,235,130 (-)Ensembl
Vero_WHO_p1.0NW_023666037198,862,999 - 198,915,680 (+)NCBI
Slc11a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248161,345,020 - 1,389,615 (+)NCBI

Position Markers
D7Wox41  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,509,551 - 131,509,676 (+)MAPPERmRatBN7.2
Rnor_6.07142,032,283 - 142,032,407NCBIRnor6.0
Rnor_5.07139,839,966 - 139,840,090UniSTSRnor5.0
RGSC_v3.47139,096,817 - 139,096,941UniSTSRGSC3.4
Celera7127,987,510 - 127,987,634UniSTS
Cytogenetic Map7q36UniSTS
RH129811  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,507,256 - 131,507,446 (+)MAPPERmRatBN7.2
Rnor_6.07142,029,988 - 142,030,177NCBIRnor6.0
Rnor_5.07139,837,671 - 139,837,860UniSTSRnor5.0
RGSC_v3.47139,094,522 - 139,094,711UniSTSRGSC3.4
Celera7127,985,215 - 127,985,404UniSTS
RH 3.4 Map71075.2UniSTS
Cytogenetic Map7q36UniSTS
RH94425  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,507,270 - 131,507,436 (+)MAPPERmRatBN7.2
Rnor_6.07142,030,002 - 142,030,167NCBIRnor6.0
Rnor_5.07139,837,685 - 139,837,850UniSTSRnor5.0
RGSC_v3.47139,094,536 - 139,094,701UniSTSRGSC3.4
Celera7127,985,229 - 127,985,394UniSTS
Cytogenetic Map7q36UniSTS
AI011296  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,506,935 - 131,507,113 (+)MAPPERmRatBN7.2
Rnor_6.07142,029,667 - 142,029,844NCBIRnor6.0
Rnor_5.07139,837,350 - 139,837,527UniSTSRnor5.0
RGSC_v3.47139,094,201 - 139,094,378UniSTSRGSC3.4
Celera7127,984,894 - 127,985,071UniSTS
RH 3.4 Map71077.6UniSTS
Cytogenetic Map7q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1290
Count of miRNA genes:359
Interacting mature miRNAs:515
Transcripts:ENSRNOT00000026531
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 2 30 40 24 18 24 2 74 35 40 11
Low 1 13 17 17 1 17 8 9 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026531   ⟹   ENSRNOP00000026531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,507,240 - 131,540,145 (-)Ensembl
Rnor_6.0 Ensembl7142,029,971 - 142,062,870 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081327   ⟹   ENSRNOP00000068880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,503,081 - 131,526,494 (-)Ensembl
Rnor_6.0 Ensembl7142,025,817 - 142,050,558 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086751   ⟹   ENSRNOP00000073199
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,503,081 - 131,527,851 (-)Ensembl
Rnor_6.0 Ensembl7142,025,815 - 142,050,578 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089912   ⟹   ENSRNOP00000068533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,511,847 - 131,540,145 (-)Ensembl
Rnor_6.0 Ensembl7142,034,728 - 142,063,212 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093762   ⟹   ENSRNOP00000091312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,503,094 - 131,538,996 (-)Ensembl
RefSeq Acc Id: NM_013173   ⟹   NP_037305
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,507,240 - 131,540,143 (-)NCBI
Rnor_6.07142,029,971 - 142,062,870 (-)NCBI
Rnor_5.07139,833,529 - 139,870,819 (-)NCBI
RGSC_v3.47139,094,505 - 139,127,427 (-)RGD
Celera7127,985,198 - 128,017,825 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242309   ⟹   XP_006242371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,503,076 - 131,540,246 (-)NCBI
Rnor_6.07142,025,812 - 142,062,891 (-)NCBI
Rnor_5.07139,833,529 - 139,870,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242311   ⟹   XP_006242373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,503,076 - 131,539,034 (-)NCBI
Rnor_6.07142,025,812 - 142,061,721 (-)NCBI
Rnor_5.07139,833,529 - 139,870,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242312   ⟹   XP_006242374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,503,076 - 131,538,263 (-)NCBI
Rnor_6.07142,025,812 - 142,061,596 (-)NCBI
Rnor_5.07139,833,529 - 139,870,819 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078495   ⟹   XP_038934423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,503,076 - 131,527,869 (-)NCBI
RefSeq Acc Id: XM_039078496   ⟹   XP_038934424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,503,076 - 131,534,463 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037305   ⟸   NM_013173
- UniProtKB: O54902 (UniProtKB/Swiss-Prot),   A0A140TAD8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242371   ⟸   XM_006242309
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006242373   ⟸   XM_006242311
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JTX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242374   ⟸   XM_006242312
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JTX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026531   ⟸   ENSRNOT00000026531
RefSeq Acc Id: ENSRNOP00000068533   ⟸   ENSRNOT00000089912
RefSeq Acc Id: ENSRNOP00000068880   ⟸   ENSRNOT00000081327
RefSeq Acc Id: ENSRNOP00000073199   ⟸   ENSRNOT00000086751
RefSeq Acc Id: XP_038934424   ⟸   XM_039078496
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934423   ⟸   XM_039078495
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000091312   ⟸   ENSRNOT00000093762

Transcriptome

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

Promoters
RGD ID:13695658
Promoter ID:EPDNEW_R6180
Type:multiple initiation site
Name:Slc11a2_1
Description:solute carrier family 11 member 2
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_6.07142,062,886 - 142,062,946EPDNEW

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)
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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)
ACI/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
ACI/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
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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 (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
F344/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
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
F344/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
FHH/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
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
FXLE16/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
FXLE18/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
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/FarMcwi (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
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
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 (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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/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
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)
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3684 AgrOrtholog
Ensembl Genes ENSRNOG00000019550 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026531 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068533 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068880 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073199 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026531 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081327 UniProtKB/TrEMBL
  ENSRNOT00000086751 UniProtKB/TrEMBL
  ENSRNOT00000089912 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7460406 IMAGE-MGC_LOAD
InterPro NRAMP_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25715 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:114348 IMAGE-MGC_LOAD
NCBI Gene 25715 ENTREZGENE
PANTHER PTHR11706 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Nramp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc11a2 PhenoGen
PRINTS NATRESASSCMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217949
TIGRFAMs nramp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JT15_RAT UniProtKB/TrEMBL
  A0A0G2JTX4 ENTREZGENE, UniProtKB/TrEMBL
  A0A140TAD8 ENTREZGENE, UniProtKB/TrEMBL
  NRAM2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4QR92_RAT UniProtKB/TrEMBL
UniProt Secondary O35172 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc11a2  solute carrier family 11 member 2  Slc11a2  solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc11a2  solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2  Slc11a2  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc11a2  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2    solute carrier family 11 member 2  Name updated 1299863 APPROVED
2002-06-10 Slc11a2  solute carrier family 11 member 2      Symbol and Name status set to approved 70586 APPROVED
2001-06-22 Nramp2  Natural resistance-associated macrophage protein 2      Symbol withdrawn, duplicate of Slc11a2 (RGD:3684) 67952 WITHDRAWN
2001-06-22 Slc11a2  Solute carrier family 11 member 2      Name updated - removed withdrawn Nramp2 text from name 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations cause hypochromic, microcytic anemia 67982
gene_disease G185R mutation causes the autosomal recessive anemic phenotype in the Belgrade (b) rat which is characterized by microcytic, hypochromic anemia associated with abnormalities in reticulocyte iron uptake and gastrointestinal iron absorption 729808
gene_expression mRNA and protein strongly expressed in kidney 67982
gene_function proton-coupled divalent metal ion transporter 67982
gene_process may provide the molecular mechanism for apical iron entry in the distal nephron and for uptake of dietary iron by the gastrointestinal tract 67982
gene_transcript two isoforms encoded by the 1IRE and 2IRE transcripts with predicted size of 61 (1IRE) and 63 kDa (2IRE) 67982