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 detoxification of cadmium ion; intracellular monoatomic cation homeostasis; and transition metal ion transport. Predicted to act upstream of or within several processes, including defense response to other organism; regulation of gene expression; and response to bacterium. Predicted to be located in late endosome membrane; lysosome; and tertiary granule membrane. Predicted to be active in bounding membrane of organelle and plasma membrane. Human ortholog(s) of this gene implicated in several diseases, including Behcet's disease; inflammatory bowel disease (multiple); leishmaniasis (multiple); rheumatoid arthritis (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: VALIDATED
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8983,406,327 - 83,417,252 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl983,406,427 - 83,417,238 (+)EnsemblGRCr8
mRatBN7.2975,957,193 - 75,968,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx984,402,352 - 84,413,166 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0989,531,293 - 89,542,107 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0987,917,487 - 87,928,297 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0981,655,590 - 81,666,697 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,655,629 - 81,666,706 (+)Ensemblrn6Rnor6.0
Rnor_5.0981,420,556 - 81,431,345 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4973,714,692 - 73,725,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera973,531,012 - 73,541,597 (+)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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  (IEA,ISO)
cellular detoxification of cadmium ion  (IEA,ISO)
defense response to bacterium  (ISO)
defense response to Gram-negative bacterium  (ISO)
defense response to protozoan  (ISO)
inflammatory response  (ISO)
intracellular iron ion homeostasis  (IBA,IEA,ISO)
intracellular manganese ion homeostasis  (IBA)
iron ion transmembrane transport  (IBA,IEA)
iron ion transport  (IEA,ISO,ISS)
L-arginine transmembrane transport  (ISO)
macrophage activation  (ISO)
manganese ion transmembrane transport  (IEA)
manganese ion transport  (IBA,IEA,ISO,ISS)
MAPK cascade  (ISO)
metal ion transport  (IEA,ISO)
MHC class II biosynthetic process  (ISO)
monoatomic ion transport  (IEA)
mRNA stabilization  (ISO)
multicellular organismal-level 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 phagocytosis  (ISO)
positive regulation of T-helper 1 type immune response  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of type II interferon production  (ISO)
proton transmembrane transport  (IEA)
respiratory burst  (ISO)
response to bacterium  (IEA,ISO)
response to lipopolysaccharide  (ISO)
response to type II interferon  (ISO)
T cell proliferation involved in immune response  (ISO)
vacuolar acidification  (ISO)
wound healing  (ISO)

Cellular Component
endosome membrane  (IBA,IEA,ISO)
late endosome  (IEA,ISO)
late endosome membrane  (IEA,ISO)
lysosomal membrane  (IBA,IEA,ISO)
lysosome  (IEA,ISO)
membrane  (IEA)
phagocytic vesicle membrane  (IBA,IEA,ISO)
plasma membrane  (IBA,IEA,ISO)
tertiary granule membrane  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. The functional SLC11A1 gene polymorphisms are associated with sarcoidosis in Turkish population. Akcakaya P, etal., Mol Biol Rep. 2011 Dec 8.
2. Granulomatous reaction to intradermal injection of lepromin (Mitsuda reaction) is linked to the human NRAMP1 gene in Vietnamese leprosy sibships. Alcais A, etal., J Infect Dis. 2000 Jan;181(1):302-8.
3. NRAMP1 (SLC11A1): a plausible candidate gene for systemic sclerosis (SSc) with interstitial lung involvement. Ates O, etal., J Clin Immunol. 2008 Jan;28(1):73-7. Epub 2007 Sep 18.
4. Genetic susceptibility to Behcet's syndrome is associated with NRAMP1 (SLC11A1) polymorphism in Turkish patients. Ates O, etal., Rheumatol Int. 2009 May;29(7):787-91. Epub 2008 Nov 8.
5. Slc11a1 (formerly Nramp1) polymorphisms and susceptibility to post-transplant lymphoproliferative disease following pediatric liver transplantation. Barshes NR, etal., Transpl Infect Dis. 2006 Jun;8(2):108-12.
6. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
7. Genetic determinants of acute inflammation regulate Salmonella infection and modulate Slc11a1 gene (formerly Nramp1) effects in selected mouse lines. Borrego A, etal., Microbes Infect. 2006 Oct;8(12-13):2766-71. Epub 2006 Sep 7.
8. CXCR1 and SLC11A1 polymorphisms affect susceptibility to cutaneous leishmaniasis in Brazil: a case-control and family-based study. Castellucci L, etal., BMC Med Genet. 2010 Jan 20;11:10.
9. A murine intraperitoneal infection model reveals that host resistance to Campylobacter jejuni is Nramp1 dependent. Champion OL, etal., Microbes Infect. 2008 Jul;10(8):922-7. Epub 2008 May 14.
10. Crohn's disease and SLC11A1 promoter polymorphism. Chermesh I, etal., Dig Dis Sci. 2007 Jul;52(7):1632-5. Epub 2007 Mar 24.
11. Genetic analysis of SLC11A1 polymorphisms in multiple sclerosis patients. Comabella M, etal., Mult Scler. 2004 Dec;10(6):618-20.
12. Evaluation of SLC11A1 as an inflammatory bowel disease candidate gene. Crawford NP, etal., BMC Med Genet. 2005 Mar 9;6:10.
13. Polymorphisms of the human NRAMP1 gene are associated with response to bacillus Calmette-Guerin immunotherapy for superficial bladder cancer. Decobert M, etal., J Urol. 2006 Apr;175(4):1506-11.
14. Genes and environment in susceptibility to visceral leishmaniasis. El-Safi S, etal., C R Biol. 2006 Nov;329(11):863-70. Epub 2006 Aug 22.
15. Susceptibility to leprosy may be conditioned by an interaction between the NRAMP1 promoter polymorphisms and the lepromin response. Ferreira FR, etal., Int J Lepr Other Mycobact Dis. 2004 Dec;72(4):457-67.
16. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
17. NRAMP1 polymorphism and viral factors in Sardinian multiple sclerosis patients. Gazouli M, etal., Can J Neurol Sci. 2008 Sep;35(4):491-4.
18. Role of functional polymorphisms of NRAMP1 gene for the development of Crohn's disease. Gazouli M, etal., Inflamm Bowel Dis. 2008 Oct;14(10):1323-30.
19. Influence of Slc11a1 (formerly Nramp1) on DSS-induced colitis in mice. Jiang HR, etal., J Leukoc Biol. 2009 Apr;85(4):703-10. Epub 2008 Dec 30.
20. In vivo RNA interference demonstrates a role for Nramp1 in modifying susceptibility to type 1 diabetes. Kissler S, etal., Nat Genet. 2006 Apr;38(4):479-83. Epub 2006 Mar 19.
21. Inflammatory bowel disease is associated with a novel promoter polymorphism of natural resistance-associated macrophage protein 1 (NRAMP1) gene. Kojima Y, etal., Tissue Antigens. 2001 Dec;58(6):379-84.
22. Population-based case-control study of alpha 1-antitrypsin and SLC11A1 in Crohn's disease and ulcerative colitis. Kotlowski R, etal., Inflamm Bowel Dis. 2008 Aug;14(8):1112-7.
23. Differential microbial clearance and immunoresponse of Balb/c (Nramp1 susceptible) and DBA2 (Nramp1 resistant) mice intracerebrally infected with Mycobacterium bovis BCG (BCG). Mazzolla R, etal., FEMS Immunol Med Microbiol. 2002 Jan 14;32(2):149-58.
24. Association of NRAMP1 polymorphism with leprosy type but not susceptibility to leprosy per se in west Africans. Meisner SJ, etal., Am J Trop Med Hyg. 2001 Dec;65(6):733-5.
25. Salmonella typhimurium persists within macrophages in the mesenteric lymph nodes of chronically infected Nramp1+/+ mice and can be reactivated by IFNgamma neutralization. Monack DM, etal., J Exp Med. 2004 Jan 19;199(2):231-41.
26. Functional polymorphism in Z-DNA-forming motif of promoter of SLC11A1 gene and type 1 diabetes in Japanese subjects: association study and meta-analysis. Nishino M, etal., Metabolism. 2005 May;54(5):628-33.
27. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
28. Linking chronic infection and autoimmune diseases: Mycobacterium avium subspecies paratuberculosis, SLC11A1 polymorphisms and type-1 diabetes mellitus. Paccagnini D, etal., PLoS One. 2009 Sep 21;4(9):e7109.
29. Systemic lupus erythematosus: association with KIR and SLC11A1 polymorphisms, ethnic predisposition and influence in clinical manifestations at onset revealed by ancestry genetic markers in an urban Brazilian population. Pedroza LS, etal., Lupus. 2011 Mar;20(3):265-73. Epub 2011 Jan 13.
30. Slc11a1 (formerly NRAMP1) gene modulates both acute inflammatory reactions and pristane-induced arthritis in mice. Peters LC, etal., Genes Immun. 2007 Jan;8(1):51-6. Epub 2006 Nov 23.
31. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
33. Comprehensive gene review and curation RGD comprehensive gene curation
34. Association of NRAMP1 promoter gene polymorphism with the susceptibility and radiological severity of rheumatoid arthritis. Rodriguez MR, etal., Tissue Antigens. 2002 Apr;59(4):311-5.
35. SLC11A1 promoter gene polymorphisms and fibrosis progression in chronic hepatitis C. Romero-Gomez M, etal., Gut. 2004 Mar;53(3):446-50.
36. Polymorphism at NRAMP1 and D2S1471 loci associated with juvenile rheumatoid arthritis. Sanjeevi CB, etal., Arthritis Rheum. 2000 Jun;43(6):1397-404.
37. Relationship between Crohn's disease, infection with Mycobacterium avium subspecies paratuberculosis and SLC11A1 gene polymorphisms in Sardinian patients. Sechi LA, etal., World J Gastroenterol. 2006 Nov 28;12(44):7161-4.
38. The Slc11a1 (Nramp1) gene controls efficacy of mycobacterial treatment of allergic asthma. Smit JJ, etal., J Immunol. 2003 Jul 15;171(2):754-60.
39. Polymorphisms of the NRAMP1 gene: distribution and susceptibility to the development of pulmonary tuberculosis in the Greek population. Stagas MK, etal., Med Sci Monit. 2011 Jan;17(1):PH1-6.
40. SLC11A1 polymorphisms in inflammatory bowel disease and Mycobacterium avium subspecies paratuberculosis status. Stewart LC, etal., World J Gastroenterol. 2010 Dec 7;16(45):5727-31.
41. Nramp1 drives an accelerated inflammatory response during Salmonella-induced colitis in mice. Valdez Y, etal., Cell Microbiol. 2009 Feb;11(2):351-62. Epub 2008 Nov 3.
42. Infection with Mycobacterium tuberculosis Beijing genotype strains is associated with polymorphisms in SLC11A1/NRAMP1 in Indonesian patients with tuberculosis. van Crevel R, etal., J Infect Dis. 2009 Dec 1;200(11):1671-4.
43. NRAMP1, VDR, HLA-DRB1, and HLA-DQB1 gene polymorphisms in susceptibility to tuberculosis among the Chinese Kazakh population: a case-control study. Wu F, etal., Biomed Res Int. 2013;2013:484535. doi: 10.1155/2013/484535. Epub 2013 Sep 1.
44. Evidence of association with type 1 diabetes in the SLC11A1 gene region. Yang JH, etal., BMC Med Genet. 2011 Apr 27;12:59.
45. NRAMP1 gene polymorphisms in patients with rheumatoid arthritis in Koreans. Yang YS, etal., J Korean Med Sci. 2000 Feb;15(1):83-7.
46. The -237C-->T promoter polymorphism of the SLC11A1 gene is associated with a protective effect in relation to inflammatory bowel disease in the South African population. 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
GRCr8983,406,327 - 83,417,252 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl983,406,427 - 83,417,238 (+)EnsemblGRCr8
mRatBN7.2975,957,193 - 75,968,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx984,402,352 - 84,413,166 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0989,531,293 - 89,542,107 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0987,917,487 - 87,928,297 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0981,655,590 - 81,666,697 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,655,629 - 81,666,706 (+)Ensemblrn6Rnor6.0
Rnor_5.0981,420,556 - 81,431,345 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4973,714,692 - 73,725,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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.p14 Ensembl2218,382,029 - 218,396,894 (+)Ensemblhg38GRCh38
GRCh372219,246,996 - 219,261,617 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362218,954,996 - 218,969,861 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342219,072,421 - 219,086,002NCBI
Celera2213,013,369 - 213,028,238 (+)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2211,100,043 - 211,114,917 (+)NCBIHuRef
CHM1_12219,253,406 - 219,268,272 (+)NCBICHM1_1
T2T-CHM13v2.02218,868,403 - 218,883,023 (+)NCBIT2T-CHM13v2.0
Slc11a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39174,414,318 - 74,429,974 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl174,414,354 - 74,425,221 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38174,375,014 - 74,386,057 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl174,375,195 - 74,386,062 (+)Ensemblmm10GRCm38
MGSCv37174,421,777 - 74,432,625 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36174,308,436 - 74,319,269 (+)NCBIMGSCv36mm8
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 (-)Ensembl
ChiLan1.0NW_00495545314,980,562 - 14,995,118 (-)NCBIChiLan1.0ChiLan1.0
SLC11A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213121,013,434 - 121,028,331 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B121,028,394 - 121,041,725 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B105,640,613 - 105,655,524 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B224,238,284 - 224,252,941 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B224,238,284 - 224,252,941 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3725,859,294 - 25,867,379 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03725,054,994 - 25,063,083 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3725,053,097 - 25,063,084 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13724,960,561 - 24,968,638 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03724,894,238 - 24,902,300 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03724,914,545 - 24,922,623 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slc11a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303174,544,696 - 174,553,261 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936569887,742 - 895,977 (+)EnsemblSpeTri2.0 Ensembl
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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604095,112,392 - 95,128,910 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc11a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248236,612,452 - 6,625,300 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248236,612,452 - 6,625,047 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Slc11a1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14147,824,608 - 147,833,328 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Slc11a1
42 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98216882386720295Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)94445825685262605Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat

Markers in Region
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
Celera973,530,668 - 73,530,841UniSTS
RGSC_v3.1973,861,330 - 73,861,503RGD
Cytogenetic Map9q33UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 158 91 90 59 92 59 6 356 192 11 136 81 92 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000057472   ⟹   ENSRNOP00000054282
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl983,406,450 - 83,417,238 (+)Ensembl
mRatBN7.2 Ensembl975,957,316 - 75,968,101 (+)Ensembl
Rnor_6.0 Ensembl981,655,696 - 81,666,701 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000080961
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
Ensembl Acc Id: ENSRNOT00000082956
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl981,662,648 - 81,663,364 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083421   ⟹   ENSRNOP00000075229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl983,406,427 - 83,413,516 (+)Ensembl
mRatBN7.2 Ensembl975,957,316 - 75,964,382 (+)Ensembl
Rnor_6.0 Ensembl981,656,116 - 81,661,658 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085699
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl981,666,211 - 81,666,683 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000088679   ⟹   ENSRNOP00000071174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl983,406,427 - 83,417,237 (+)Ensembl
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: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8983,406,450 - 83,417,252 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8983,406,327 - 83,417,252 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8983,406,393 - 83,417,252 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8983,411,300 - 83,417,252 (+)NCBI
mRatBN7.2975,962,164 - 75,968,064 (+)NCBI
RefSeq Acc Id: NP_001026828   ⟸   NM_001031658
- UniProtKB: Q496Z6 (UniProtKB/Swiss-Prot),   P70553 (UniProtKB/Swiss-Prot),   F1LSN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245281   ⟸   XM_006245219
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A4H2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245282   ⟸   XM_006245220
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000054282   ⟸   ENSRNOT00000057472
Ensembl Acc Id: ENSRNOP00000075229   ⟸   ENSRNOT00000083421
Ensembl 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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1601463 AgrOrtholog
BioCyc Gene G2FUF-27137 BioCyc
Ensembl Genes ENSRNOG00000014956 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000057472 ENTREZGENE
  ENSRNOT00000088679 ENTREZGENE
IMAGE_CLONE IMAGE:7932285 IMAGE-MGC_LOAD
InterPro NRAMP_fam UniProtKB/Swiss-Prot
KEGG Report rno:316519 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124692 IMAGE-MGC_LOAD
NCBI Gene 316519 ENTREZGENE
PANTHER NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 1 UniProtKB/Swiss-Prot
  PTHR11706 UniProtKB/Swiss-Prot
Pfam Nramp UniProtKB/Swiss-Prot
PhenoGen Slc11a1 PhenoGen
PRINTS NATRESASSCMP UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014956 RatGTEx
UniProt A0A0G2JZT3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KA24_RAT UniProtKB/TrEMBL
  A0A8I6A4H2 ENTREZGENE
  A6JVU4 ENTREZGENE, UniProtKB/TrEMBL
  A6JVU5_RAT UniProtKB/TrEMBL
  F1LSN8 ENTREZGENE, UniProtKB/TrEMBL
  NRAM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q496Z6 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