Slc11a1 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Slc11a1provided by MGI
Official Full Name: solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1provided by MGI
Primary source: MGI:MGI:1345275
See related: Ensembl:ENSMUSG00000026177 AllianceGenome:MGI:1345275
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Bcg; Ity; Lsh; ity; Ity1; Nramp; Nramp1
Summary: Enables manganese ion transmembrane transporter activity. Involved in metal ion export. Acts upstream of or within several processes, including cation homeostasis; defense response to other organism; and positive regulation of macromolecule metabolic process. Located in cytoplasmic vesicle and lysosome. Is expressed in several structures, including brain; gut; hemolymphoid system gland; liver and biliary system; and reproductive system. 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). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in spleen adult (RPKM 37.5), mammary gland adult (RPKM 13.7) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 C3; 1 38.54 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (74414318..74429974)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (74375014..74386057)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Slc11a1 gene polymorphism influences dextran sulfate sodium (DSS)-induced colitis in a murine model of acute inflammation.
Title: Slc11a1 gene polymorphism influences dextran sulfate sodium (DSS)-induced colitis in a murine model of acute inflammation.
Nrf2 Regulates Granuloma Formation and Macrophage Activation during Mycobacterium avium Infection via Mediating Nramp1 and HO-1 Expressions.
Title: Nrf2 Regulates Granuloma Formation and Macrophage Activation during Mycobacterium avium Infection via Mediating Nramp1 and HO-1 Expressions.
Leishmania infection triggers hepcidin-mediated proteasomal degradation of Nramp1 to increase phagolysosomal iron availability.
Title: Leishmania infection triggers hepcidin-mediated proteasomal degradation of Nramp1 to increase phagolysosomal iron availability.
A specific role for Lsh in guarding and preserving chromatin structure to prevent access to tissue specific enhancers or regulatory regions.Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy.
Title: The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors.
findings identify deprivation of the main group metal magnesium as the main resistance mechanism of SLC11A1 against Salmonella
Title: Host resistance factor SLC11A1 restricts Salmonella growth through magnesium deprivation.
SLC11A1 polymorphisms are associated with with susceptibility to leishmaniasis.
Title: Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis.
Our data demonstrated the fine-tuning roles of Slc11a1 alleles modulating macrophage activation, and consequent pristane-induced arthritis susceptibility.
Title: Slc11a1 (Nramp-1) gene modulates immune-inflammation genes in macrophages during pristane-induced arthritis in mice.
Here, the authors show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. The results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases.
Title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes.
discrete, anatomically localized host resistance is conferred by Nramp1 expression; restriction of systemic bacterial growth in the spleen is enhanced by Nramp1 expression
Title: Temporal and anatomical host resistance to chronic Salmonella infection is quantitatively dictated by Nramp1 and influenced by host genetic background.
Data shows that Lsh plays an essential Dnmt3b-independent role to ensure that the host genome integrity is protected from potentially deleterious LTR retroelements.
Title: Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.

Submit: New GeneRIF Correction See all GeneRIFs (67)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (1) 1 citation
Targeted (1) 1 citation
Not Applicable (1) 1 citation
Endonuclease-mediated (4)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Slc11a1 (e-PCR), detects polymorphism
- UniSTS:144409

D1Mcg4 (e-PCR), detects polymorphism
- UniSTS:142239

Slc11a1 (e-PCR), detects polymorphism
- UniSTS:546991

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables cadmium ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables iron ion transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables manganese ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables manganese ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables manganese ion transmembrane transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables manganese ion transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables metal cation:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal cation:proton antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables metal cation:proton antiporter activity	ISO Inferred from Sequence Orthology more info
enables metal ion transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables transition metal ion transmembrane transporter activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within L-arginine transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within MHC class II biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within T cell cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within T cell proliferation involved in immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within activation of protein kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within antigen processing and presentation of peptide antigen	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cadmium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in cellular detoxification of cadmium ion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within defense response to Gram-negative bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to protozoan	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within interleukin-2 production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within interleukin-3 production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intracellular iron ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular iron ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in iron ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in iron ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in iron ion transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within macrophage activation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within macrophage activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in manganese ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in manganese ion transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within manganese ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in manganese ion transport	ISO Inferred from Sequence Orthology more info
involved_in metal ion transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organismal-level iron ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nitrite transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within phagocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of T-helper 1 type immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of dendritic cell antigen processing and presentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of phagocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of type II interferon production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within respiratory burst	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to lipopolysaccharide	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within response to type II interferon	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of type II interferon production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vacuolar acidification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within wound healing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in endosome	IEA Inferred from Electronic Annotation more info
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IMP Inferred from Mutant Phenotype more info	PubMed
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in phagocytic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagocytic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic vesicle membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in phagocytic vesicle membrane	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in tertiary granule membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: natural resistance-associated macrophage protein 1

Names: NRAMP 1; host resistance locus Bcg/Ity/Lsh; solute carrier family 11 member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_013612.2 → NP_038640.2 natural resistance-associated macrophage protein 1

See identical proteins and their annotated locations for NP_038640.2

Status: VALIDATED

Source sequence(s)

AK171393, BB873183

Consensus CDS

CCDS15047.1

UniProtKB/Swiss-Prot

P41251, Q3TB84

UniProtKB/TrEMBL

A0A087WNR0

Related

ENSMUSP00000027368.6, ENSMUST00000027368.6

Conserved Domains (1) summary

TIGR01197
Location:53 → 453

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

74414318..74429974

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036162734.1 → XP_036018627.1 natural resistance-associated macrophage protein 1 isoform X1

UniProtKB/Swiss-Prot

P41251, Q3TB84

UniProtKB/TrEMBL

A0A087WNR0

Conserved Domains (1) summary

TIGR01197
Location:53 → 453

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
XM_036162732.1 → XP_036018625.1 natural resistance-associated macrophage protein 1 isoform X1

UniProtKB/Swiss-Prot

P41251, Q3TB84

UniProtKB/TrEMBL

A0A087WNR0

Conserved Domains (1) summary

TIGR01197
Location:53 → 453

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
XM_036162735.1 → XP_036018628.1 natural resistance-associated macrophage protein 1 isoform X1

UniProtKB/Swiss-Prot

P41251, Q3TB84

UniProtKB/TrEMBL

A0A087WNR0

Conserved Domains (1) summary

TIGR01197
Location:53 → 453

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
XM_006495774.2 → XP_006495837.1 natural resistance-associated macrophage protein 1 isoform X2

UniProtKB/TrEMBL

A0A087WNR0

Conserved Domains (1) summary

TIGR01197
Location:1 → 389

nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters