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

Gene ID: 6556, updated on 9-Oct-2021

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
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Genomic context

See SLC11A1 in Genome Data Viewer
Location:
2q35
Exon count:
16
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218381766..218396894)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219246996..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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Buruli ulcer, susceptibility to
MedGen: C1864868 OMIM: 610446 GeneReviews: Not available
Compare labs
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
GeneReviews: Not available
Mycobacterium tuberculosis, susceptibility to
MedGen: C1834752 OMIM: 607948 GeneReviews: Not available
Compare labs

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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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.

Genomic

  1. NG_012128.1 RefSeqGene

    Range
    5245..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 Updated Annotation Release 109.20210514

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.
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