Slc11a1 (solute carrier family 11 member 1) - Rat Genome Database

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Gene: Slc11a1 (solute carrier family 11 member 1) Rattus norvegicus
Analyze
Symbol: Slc11a1
Name: solute carrier family 11 member 1
RGD ID: 1601463
Description: Predicted to enable metal ion transmembrane transporter activity and protein homodimerization activity. Predicted to be involved in cellular transition metal ion homeostasis; metal ion transport; and response to lipopolysaccharide. Predicted to act upstream of or within several processes, including cation transport; defense response to other organism; and positive regulation of macromolecule metabolic process. Predicted to be located in cytoplasmic vesicle and lysosome. Predicted to be active in phagocytic vesicle membrane and plasma membrane. Human ortholog(s) of this gene implicated in several diseases, including Buruli ulcer disease; autoimmune disease (multiple); inflammatory bowel disease (multiple); leishmaniasis (multiple); and tuberculosis (multiple). Orthologous to human SLC11A1 (solute carrier family 11 member 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Bcg; Itg; Lsh; MGC124692; natural resistance associated macrophage protein 1; natural resistance-associated macrophage protein 1; NRAMP 1; Nramp1; solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1; solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.2975,957,193 - 75,968,115 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)Ensembl
Rnor_6.0981,655,590 - 81,666,697 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,655,629 - 81,666,706 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,420,556 - 81,431,345 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4973,714,692 - 73,725,523 (+)NCBIRGSC3.4rn4RGSC3.4
Celera973,531,012 - 73,541,597 (+)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase activity  (ISO)
antigen processing and presentation of peptide antigen  (ISO)
biological_process  (ND)
cadmium ion transmembrane transport  (ISO)
cellular cadmium ion homeostasis  (IBA,ISO)
cellular iron ion homeostasis  (IBA,ISO)
defense response to bacterium  (ISO)
defense response to Gram-negative bacterium  (ISO)
defense response to protozoan  (ISO)
establishment of localization in cell  (ISO)
inflammatory response  (ISO)
iron ion homeostasis  (IEA,ISO)
iron ion transmembrane transport  (IEA)
iron ion transport  (IEA,ISO)
L-arginine transmembrane transport  (ISO)
macrophage activation  (ISO)
manganese ion transmembrane transport  (IEA)
manganese ion transport  (ISO)
MAPK cascade  (ISO)
metal ion transport  (ISO)
MHC class II biosynthetic process  (ISO)
mRNA stabilization  (ISO)
multicellular organismal iron ion homeostasis  (ISO)
negative regulation of cytokine production  (ISO)
nitrite transport  (ISO)
phagocytosis  (ISO)
positive regulation of cytokine production  (ISO)
positive regulation of dendritic cell antigen processing and presentation  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of interferon-gamma production  (ISO)
positive regulation of phagocytosis  (ISO)
positive regulation of T-helper 1 type immune response  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
proton transmembrane transport  (IEA)
respiratory burst  (ISO)
response to bacterium  (ISO)
response to interferon-gamma  (ISO)
response to lipopolysaccharide  (IBA,ISO)
T cell proliferation involved in immune response  (ISO)
vacuolar acidification  (ISO)
wound healing  (ISO)

Cellular Component

References

References - curated
1. Akcakaya P, etal., Mol Biol Rep. 2011 Dec 8.
2. Alcais A, etal., J Infect Dis. 2000 Jan;181(1):302-8.
3. Ates O, etal., J Clin Immunol. 2008 Jan;28(1):73-7. Epub 2007 Sep 18.
4. Ates O, etal., Rheumatol Int. 2009 May;29(7):787-91. Epub 2008 Nov 8.
5. Barshes NR, etal., Transpl Infect Dis. 2006 Jun;8(2):108-12.
6. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
7. Borrego A, etal., Microbes Infect. 2006 Oct;8(12-13):2766-71. Epub 2006 Sep 7.
8. Castellucci L, etal., BMC Med Genet. 2010 Jan 20;11:10.
9. Champion OL, etal., Microbes Infect. 2008 Jul;10(8):922-7. Epub 2008 May 14.
10. Chermesh I, etal., Dig Dis Sci. 2007 Jul;52(7):1632-5. Epub 2007 Mar 24.
11. Comabella M, etal., Mult Scler. 2004 Dec;10(6):618-20.
12. Crawford NP, etal., BMC Med Genet. 2005 Mar 9;6:10.
13. Decobert M, etal., J Urol. 2006 Apr;175(4):1506-11.
14. El-Safi S, etal., C R Biol. 2006 Nov;329(11):863-70. Epub 2006 Aug 22.
15. Ferreira FR, etal., Int J Lepr Other Mycobact Dis. 2004 Dec;72(4):457-67.
16. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
17. Gazouli M, etal., Can J Neurol Sci. 2008 Sep;35(4):491-4.
18. Gazouli M, etal., Inflamm Bowel Dis. 2008 Oct;14(10):1323-30.
19. Jiang HR, etal., J Leukoc Biol. 2009 Apr;85(4):703-10. Epub 2008 Dec 30.
20. Kissler S, etal., Nat Genet. 2006 Apr;38(4):479-83. Epub 2006 Mar 19.
21. Kojima Y, etal., Tissue Antigens. 2001 Dec;58(6):379-84.
22. Kotlowski R, etal., Inflamm Bowel Dis. 2008 Aug;14(8):1112-7.
23. Mazzolla R, etal., FEMS Immunol Med Microbiol. 2002 Jan 14;32(2):149-58.
24. Meisner SJ, etal., Am J Trop Med Hyg. 2001 Dec;65(6):733-5.
25. Monack DM, etal., J Exp Med. 2004 Jan 19;199(2):231-41.
26. Nishino M, etal., Metabolism. 2005 May;54(5):628-33.
27. OMIM Disease Annotation Pipeline
28. Paccagnini D, etal., PLoS One. 2009 Sep 21;4(9):e7109.
29. Pedroza LS, etal., Lupus. 2011 Mar;20(3):265-73. Epub 2011 Jan 13.
30. Peters LC, etal., Genes Immun. 2007 Jan;8(1):51-6. Epub 2006 Nov 23.
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. RGD comprehensive gene curation
34. Rodriguez MR, etal., Tissue Antigens. 2002 Apr;59(4):311-5.
35. Romero-Gomez M, etal., Gut. 2004 Mar;53(3):446-50.
36. Sanjeevi CB, etal., Arthritis Rheum. 2000 Jun;43(6):1397-404.
37. Sechi LA, etal., World J Gastroenterol. 2006 Nov 28;12(44):7161-4.
38. Smit JJ, etal., J Immunol. 2003 Jul 15;171(2):754-60.
39. Stagas MK, etal., Med Sci Monit. 2011 Jan;17(1):PH1-6.
40. Stewart LC, etal., World J Gastroenterol. 2010 Dec 7;16(45):5727-31.
41. Valdez Y, etal., Cell Microbiol. 2009 Feb;11(2):351-62. Epub 2008 Nov 3.
42. van Crevel R, etal., J Infect Dis. 2009 Dec 1;200(11):1671-4.
43. Wu F, etal., Biomed Res Int. 2013;2013:484535. doi: 10.1155/2013/484535. Epub 2013 Sep 1.
44. Yang JH, etal., BMC Med Genet. 2011 Apr 27;12:59.
45. Yang YS, etal., J Korean Med Sci. 2000 Feb;15(1):83-7.
46. Zaahl MG, etal., Int J Colorectal Dis. 2006 Jul;21(5):402-8. Epub 2005 Jul 30.
Additional References at PubMed
PMID:385184   PMID:606434   PMID:1541907   PMID:6358358   PMID:7561513   PMID:7650477   PMID:7717395   PMID:8033407   PMID:8301134   PMID:8490962   PMID:8529105   PMID:8537108  
PMID:8875897   PMID:9009318   PMID:9034150   PMID:9176118   PMID:9261342   PMID:9271100   PMID:9461570   PMID:9670047   PMID:9824471   PMID:10065630   PMID:10678911   PMID:11067873  
PMID:11903051   PMID:12070036   PMID:12429222   PMID:12477932   PMID:15489334   PMID:16470178   PMID:16510578   PMID:16905747   PMID:17097837   PMID:17620357   PMID:17932044   PMID:18045875  
PMID:18285491   PMID:18456389   PMID:18984740   PMID:19321419  


Genomics

Comparative Map Data
Slc11a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2975,957,193 - 75,968,115 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)Ensembl
Rnor_6.0981,655,590 - 81,666,697 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,655,629 - 81,666,706 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,420,556 - 81,431,345 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4973,714,692 - 73,725,523 (+)NCBIRGSC3.4rn4RGSC3.4
Celera973,531,012 - 73,541,597 (+)NCBICelera
Cytogenetic Map9q33NCBI
SLC11A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382218,382,273 - 218,396,894 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2218,382,029 - 218,396,894 (+)EnsemblGRCh38hg38GRCh38
GRCh372219,246,996 - 219,261,617 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362218,954,996 - 218,969,861 (+)NCBINCBI36hg18NCBI36
Build 342219,072,421 - 219,086,002NCBI
Celera2213,013,369 - 213,028,238 (+)NCBI
Cytogenetic Map2q35NCBI
HuRef2211,100,043 - 211,114,917 (+)NCBIHuRef
CHM1_12219,253,406 - 219,268,272 (+)NCBICHM1_1
Slc11a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39174,414,318 - 74,429,974 (+)NCBIGRCm39mm39
GRCm39 Ensembl174,414,354 - 74,425,221 (+)Ensembl
GRCm38174,375,014 - 74,386,057 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl174,375,195 - 74,386,062 (+)EnsemblGRCm38mm10GRCm38
MGSCv37174,421,777 - 74,432,625 (+)NCBIGRCm37mm9NCBIm37
MGSCv36174,308,436 - 74,319,269 (+)NCBImm8
Celera174,932,506 - 74,943,551 (+)NCBICelera
Cytogenetic Map1C3NCBI
cM Map138.54NCBI
Slc11a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545314,980,562 - 14,995,608 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545314,980,562 - 14,995,118 (-)NCBIChiLan1.0ChiLan1.0
SLC11A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B224,238,284 - 224,252,941 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B224,238,284 - 224,252,941 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B105,640,613 - 105,655,524 (+)NCBIMhudiblu_PPA_v0panPan3
SLC11A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13725,039,203 - 25,047,461 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3725,038,360 - 25,047,282 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3725,859,294 - 25,867,379 (+)NCBI
ROS_Cfam_1.03725,054,994 - 25,063,083 (+)NCBI
ROS_Cfam_1.0 Ensembl3725,053,097 - 25,063,084 (+)Ensembl
UMICH_Zoey_3.13724,960,561 - 24,968,638 (+)NCBI
UNSW_CanFamBas_1.03724,894,238 - 24,902,300 (+)NCBI
UU_Cfam_GSD_1.03724,914,545 - 24,922,623 (+)NCBI
Slc11a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303174,544,696 - 174,553,261 (+)NCBI
SpeTri2.0NW_004936569888,309 - 895,991 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC11A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15120,433,952 - 120,446,396 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115120,434,100 - 120,446,396 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215133,452,820 - 133,454,896 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC11A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110104,276,553 - 104,288,466 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604095,112,392 - 95,128,910 (-)NCBIVero_WHO_p1.0
Slc11a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248236,612,452 - 6,625,047 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Got99  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2975,956,971 - 75,957,145 (+)MAPPERmRatBN7.2
Rnor_6.0981,655,352 - 81,655,525NCBIRnor6.0
Rnor_5.0981,420,291 - 81,420,464UniSTSRnor5.0
RGSC_v3.4973,714,348 - 73,714,521RGDRGSC3.4
RGSC_v3.4973,714,348 - 73,714,521UniSTSRGSC3.4
RGSC_v3.1973,861,330 - 73,861,503RGD
Celera973,530,668 - 73,530,841UniSTS
Cytogenetic Map9q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95584784177026453Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95662771378595166Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:125
Count of miRNA genes:96
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000057472
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 6 4 11 4 1 9
Low 3 33 47 33 8 33 8 11 66 35 31 2 8
Below cutoff 10 4 4 4 6 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057472   ⟹   ENSRNOP00000054282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)Ensembl
Rnor_6.0 Ensembl981,655,696 - 81,666,701 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080961
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl975,957,612 - 75,968,101 (+)Ensembl
Rnor_6.0 Ensembl981,657,790 - 81,663,030 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl981,662,648 - 81,663,364 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083421   ⟹   ENSRNOP00000075229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl975,957,316 - 75,964,382 (+)Ensembl
Rnor_6.0 Ensembl981,656,116 - 81,661,658 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl981,666,211 - 81,666,683 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088679   ⟹   ENSRNOP00000071174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)Ensembl
Rnor_6.0 Ensembl981,655,629 - 81,666,706 (+)Ensembl
RefSeq Acc Id: NM_001031658   ⟹   NP_001026828
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2975,957,316 - 75,968,115 (+)NCBI
Rnor_6.0981,655,696 - 81,666,697 (+)NCBI
Rnor_5.0981,420,556 - 81,431,345 (+)NCBI
RGSC_v3.4973,714,692 - 73,725,523 (+)RGD
Celera973,531,012 - 73,541,597 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245219   ⟹   XP_006245281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2975,957,193 - 75,968,062 (+)NCBI
Rnor_6.0981,655,590 - 81,666,579 (+)NCBI
Rnor_5.0981,420,556 - 81,431,345 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006245220   ⟹   XP_006245282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2975,957,303 - 75,968,062 (+)NCBI
Rnor_6.0981,655,693 - 81,666,579 (+)NCBI
Rnor_5.0981,420,556 - 81,431,345 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083672   ⟹   XP_038939600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2975,962,164 - 75,968,064 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001026828   ⟸   NM_001031658
- UniProtKB: P70553 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245281   ⟸   XM_006245219
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006245282   ⟸   XM_006245220
- Peptide Label: isoform X2
- UniProtKB: A0A0G2JZT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054282   ⟸   ENSRNOT00000057472
RefSeq Acc Id: ENSRNOP00000075229   ⟸   ENSRNOT00000083421
RefSeq Acc Id: ENSRNOP00000071174   ⟸   ENSRNOT00000088679
RefSeq Acc Id: XP_038939600   ⟸   XM_039083672
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70553-F1-model_v2 AlphaFold P70553 1-507 view protein structure

Transcriptome

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

Promoters
RGD ID:13696750
Promoter ID:EPDNEW_R7275
Type:single initiation site
Name:Slc11a1_1
Description:solute carrier family 11 member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0981,655,725 - 81,655,785EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 81661623 81661624 A G snv CDR, COP/CrCrl (MCW & UW), SR/JrHsd (MCW), WKY/N (MCW), LN/MavRrrc (RGD), LL/MavRrrc (RGD), WKY/N (2020), WKY/NCrl (RGD), WKY/NHsd (RGD), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), SR/JrHsd (2020), WKY/NCrl (2019), SR/JrHsd (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 81426271 81426272 A G snv COP/CrCrl (MCW & UW), SR/JrHsd (MCW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), SDLEF7/Barth (UDEL), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SR/JrHsd (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 73720449 73720450 A G snv SR/JrHsd (MCW), WKY/N (KNAW), COP/CrCrl (MCW & UW), WKY/NHsd (ICL), LN/MavRrrc (ICL), SR/JrHsd (ICL), WKY/NCrl (ICL), LL/MavRrrc (ICL)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 75963044 75963045 A G snv LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), WKY/N (2020), WKY/NCrl (2019), SR/JrHsd (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1601463 AgrOrtholog
BioCyc Gene G2FUF-27137 BioCyc
Ensembl Genes ENSRNOG00000014956 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000054282 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071174 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075229 UniProtKB/TrEMBL
  ENSRNOP00000088138 ENTREZGENE
Ensembl Transcript ENSRNOT00000057472 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080961 ENTREZGENE
  ENSRNOT00000083421 UniProtKB/TrEMBL
  ENSRNOT00000088679 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7932285 IMAGE-MGC_LOAD
InterPro NRAMP_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316519 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124692 IMAGE-MGC_LOAD
NCBI Gene 316519 ENTREZGENE
PANTHER PTHR11706 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Nramp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc11a1 PhenoGen
PRINTS NATRESASSCMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs nramp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZT3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KA24_RAT UniProtKB/TrEMBL
  F1LSN8_RAT UniProtKB/TrEMBL
  NRAM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q496Z6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc11a1  solute carrier family 11 member 1  Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1  Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-21 Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1      Symbol and Name status set to provisional 70820 PROVISIONAL