Format

Send to:

Choose Destination

SLC11A1 solute carrier family 11 member 1 [ Homo sapiens (human) ]

Gene ID: 6556, updated on 17-Jun-2019

Summary

Official Symbol
SLC11A1provided by HGNC
Official Full Name
solute carrier family 11 member 1provided by HGNC
Primary source
HGNC:HGNC:10907
See related
Ensembl:ENSG00000018280 MIM:600266
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LSH; NRAMP; NRAMP1
Summary
This gene is a member of the solute carrier family 11 (proton-coupled divalent metal ion transporters) family and encodes a multi-pass membrane protein. The protein functions as a divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Mutations in this gene have been associated with susceptibility to infectious diseases such as tuberculosis and leprosy, and inflammatory diseases such as rheumatoid arthritis and Crohn disease. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]
Expression
Biased expression in lung (RPKM 10.4), appendix (RPKM 8.8) and 7 other tissues See more
Orthologs

Genomic context

See SLC11A1 in Genome Data Viewer
Location:
2q35
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218381766..218396894)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219246752..219261617)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CATIP antisense RNA 2 Neighboring gene ribosomal protein L19 pseudogene 5 Neighboring gene CATIP antisense RNA 1 Neighboring gene ciliogenesis associated TTC17 interacting protein Neighboring gene CTD small phosphatase 1 Neighboring gene microRNA 26b Neighboring gene villin 1 Neighboring gene ubiquitin specific peptidase 37

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Buruli ulcer, susceptibility to
MedGen: C1864868 OMIM: 610446 GeneReviews: Not available
Compare labs
Mycobacterium tuberculosis, susceptibility to
MedGen: C1834752 OMIM: 607948 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
NHGRI GWA Catalog

Pathways from BioSystems

  • Antimicrobial peptides, organism-specific biosystem (from REACTOME)
    Antimicrobial peptides, organism-specific biosystemAntimicrobial peptides (AMPs) are small molecular weight proteins with broad spectrum of antimicrobial activity against bacteria, viruses, and fungi (Zasloff M 2002; Radek K & Gallo R 2007). The majo...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Ion influx/efflux at host-pathogen interface, organism-specific biosystem (from REACTOME)
    Ion influx/efflux at host-pathogen interface, organism-specific biosystemEssential metal ions act as co-factors that enable enzymes to catalyse a wider range of chemical transformations than would be achievable using solely organic catalysts. The precise metal requirement...
  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Metal ion SLC transporters, organism-specific biosystem (from REACTOME)
    Metal ion SLC transporters, organism-specific biosystemSix SLC gene families encode proteins which mediate transport of metals. The families are SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41 (He L et al, 2009; Bressler JP et al, 2007).
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • ROS, RNS production in phagocytes, organism-specific biosystem (from REACTOME)
    ROS, RNS production in phagocytes, organism-specific biosystemThe first line of defense against infectious agents involves an active recruitment of phagocytes to the site of infection. Recruited cells include polymorhonuclear (PMN) leukocytes (i.e., neutrophils...
  • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
    SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules
  • Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystem (from REACTOME)
    Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystemHexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse acro...
  • Validated targets of C-MYC transcriptional repression, organism-specific biosystem (from Pathway Interaction Database)
    Validated targets of C-MYC transcriptional repression, organism-specific biosystem
    Validated targets of C-MYC transcriptional repression

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadmium ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
iron ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
manganese ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
manganese ion transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion:proton antiporter activity IGI
Inferred from Genetic Interaction
more info
PubMed 
metal ion:proton antiporter activity TAS
Traceable Author Statement
more info
 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
transition metal ion transmembrane transporter activity IGI
Inferred from Genetic Interaction
more info
PubMed 
Process Evidence Code Pubs
L-arginine transport IEA
Inferred from Electronic Annotation
more info
 
MHC class II biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
T cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
T cell proliferation involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
activation of protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
antigen processing and presentation of peptide antigen ISS
Inferred from Sequence or Structural Similarity
more info
 
antimicrobial humoral response TAS
Traceable Author Statement
more info
 
cadmium ion transmembrane transport IGI
Inferred from Genetic Interaction
more info
PubMed 
cell redox homeostasis TAS
Traceable Author Statement
more info
 
cellular cadmium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular cadmium ion homeostasis IGI
Inferred from Genetic Interaction
more info
PubMed 
cellular iron ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response to Gram-negative bacterium ISS
Inferred from Sequence or Structural Similarity
more info
 
defense response to bacterium ISS
Inferred from Sequence or Structural Similarity
more info
 
defense response to protozoan ISS
Inferred from Sequence or Structural Similarity
more info
 
divalent metal ion export ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
interleukin-2 production ISS
Inferred from Sequence or Structural Similarity
more info
 
interleukin-3 production ISS
Inferred from Sequence or Structural Similarity
more info
 
iron ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
iron ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
iron ion transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA stabilization ISS
Inferred from Sequence or Structural Similarity
more info
 
macrophage activation ISS
Inferred from Sequence or Structural Similarity
more info
 
manganese ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
manganese ion transport ISS
Inferred from Sequence or Structural Similarity
more info
 
multicellular organismal iron ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
nitrite transport ISS
Inferred from Sequence or Structural Similarity
more info
 
phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T-helper 1 type immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendritic cell antigen processing and presentation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interferon-gamma production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
respiratory burst ISS
Inferred from Sequence or Structural Similarity
more info
 
response to bacterium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
response to interferon-gamma ISS
Inferred from Sequence or Structural Similarity
more info
 
response to lipopolysaccharide IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to lipopolysaccharide ISS
Inferred from Sequence or Structural Similarity
more info
 
vacuolar acidification ISS
Inferred from Sequence or Structural Similarity
more info
 
wound healing ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
 
integral component of plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
late endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
late endosome membrane TAS
Traceable Author Statement
more info
 
lysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
phagocytic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phagocytic vesicle membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
tertiary granule membrane IDA
Inferred from Direct Assay
more info
PubMed 
tertiary granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
natural resistance-associated macrophage protein 1
Names
NRAMP 1
solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1
solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1
solute carrier family 11 (sodium/phosphate symporters), member 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_012128.1 RefSeqGene

    Range
    5001..19866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000578.4NP_000569.3  natural resistance-associated macrophage protein 1

    See identical proteins and their annotated locations for NP_000569.3

    Status: REVIEWED

    Source sequence(s)
    AC021016, CA307182, DB284801, L32185
    Consensus CDS
    CCDS2415.1
    UniProtKB/Swiss-Prot
    P49279
    UniProtKB/TrEMBL
    A0A024R474
    Related
    ENSP00000233202.6, ENST00000233202.11
    Conserved Domains (2) summary
    TIGR01197
    Location:56456
    nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
    pfam01566
    Location:78463
    Nramp; Natural resistance-associated macrophage protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    218381766..218396894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511684.3XP_011509986.1  natural resistance-associated macrophage protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011509986.1

    Conserved Domains (2) summary
    pfam01566
    Location:59354
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:59347
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_005246794.4XP_005246851.1  natural resistance-associated macrophage protein 1 isoform X4

    See identical proteins and their annotated locations for XP_005246851.1

    UniProtKB/Swiss-Prot
    P49279
    Conserved Domains (2) summary
    pfam01566
    Location:16345
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:14338
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. XM_017004765.2XP_016860254.1  natural resistance-associated macrophage protein 1 isoform X1

  4. XM_017004766.2XP_016860255.1  natural resistance-associated macrophage protein 1 isoform X2

    UniProtKB/Swiss-Prot
    P49279
    Conserved Domains (2) summary
    TIGR01197
    Location:1389
    nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
    pfam01566
    Location:11396
    Nramp; Natural resistance-associated macrophage protein
  5. XM_011511685.3XP_011509987.1  natural resistance-associated macrophage protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011509987.1

    Conserved Domains (2) summary
    pfam01566
    Location:59354
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:59347
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. XM_006712709.4XP_006712772.1  natural resistance-associated macrophage protein 1 isoform X4

    See identical proteins and their annotated locations for XP_006712772.1

    UniProtKB/Swiss-Prot
    P49279
    Conserved Domains (2) summary
    pfam01566
    Location:16345
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:14338
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  7. XM_005246793.4XP_005246850.1  natural resistance-associated macrophage protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005246850.1

    UniProtKB/Swiss-Prot
    P49279
    Conserved Domains (2) summary
    TIGR01197
    Location:1389
    nramp; NRAMP (natural resistance-associated macrophage protein) metal ion transporters
    pfam01566
    Location:11396
    Nramp; Natural resistance-associated macrophage protein
  8. XM_006712710.4XP_006712773.1  natural resistance-associated macrophage protein 1 isoform X4

    See identical proteins and their annotated locations for XP_006712773.1

    UniProtKB/Swiss-Prot
    P49279
    Conserved Domains (2) summary
    pfam01566
    Location:16345
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:14338
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  9. XM_006712711.4XP_006712774.1  natural resistance-associated macrophage protein 1 isoform X6

    Conserved Domains (2) summary
    pfam01566
    Location:1314
    Nramp; Natural resistance-associated macrophage protein
    cl00456
    Location:1307
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  10. XM_017004767.2XP_016860256.1  natural resistance-associated macrophage protein 1 isoform X5

RNA

  1. XR_427108.4 RNA Sequence

  2. XR_427107.3 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001032220.1: Suppressed sequence

    Description
    NM_001032220.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center