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

    Gene ID: 6556, updated on 3-Dec-2024

    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; AllianceGenome:HGNC:10907
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC11A1 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218382273..218396894)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218868403..218883023)
    RS_2024_09 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 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219221475-219221986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12315 Neighboring gene ribosomal protein L19 pseudogene 5 Neighboring gene CATIP antisense RNA 1 Neighboring gene ciliogenesis associated TTC17 interacting protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219257303-219257972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219258642-219259310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219259311-219259979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17124 Neighboring gene CTD small phosphatase 1 Neighboring gene microRNA 26b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219289129-219289629 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:219290512-219290729 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
    Mycobacterium tuberculosis, susceptibility to
    MedGen: C1834752 OMIM: 607948 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in L-arginine transmembrane 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 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 detoxification of cadmium ion IGI
    Inferred from Genetic Interaction
    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 establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular iron ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in manganese ion transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in manganese ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metal ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in multicellular organismal-level 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
     
    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
     
    acts_upstream_of_or_within positive regulation of type II interferon production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of type II interferon production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    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 lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to type II interferon 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
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    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
     
    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
     
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    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
    Leishmaniasis resistance
    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)

    NEW Try the new Transcript table

    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
      C0H5Y3, P49279
      UniProtKB/TrEMBL
      B4E0J2
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      218382273..218396894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005246793.5XP_005246850.1  natural resistance-associated macrophage protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005246850.1

      UniProtKB/TrEMBL
      B4E0J2
      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
    2. XM_006712711.5XP_006712774.1  natural resistance-associated macrophage protein 1 isoform X4

      UniProtKB/TrEMBL
      B4E0J2
      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
    3. XM_047445574.1XP_047301530.1  natural resistance-associated macrophage protein 1 isoform X3

      UniProtKB/TrEMBL
      B4DQ73, B9ZVN3
    4. XM_047445575.1XP_047301531.1  natural resistance-associated macrophage protein 1 isoform X5

    5. XM_017004766.3XP_016860255.1  natural resistance-associated macrophage protein 1 isoform X1

      UniProtKB/TrEMBL
      B4E0J2
      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
    6. XM_047445573.1XP_047301529.1  natural resistance-associated macrophage protein 1 isoform X2

      UniProtKB/TrEMBL
      B4E0J2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      218868403..218883023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343500.1XP_054199475.1  natural resistance-associated macrophage protein 1 isoform X1

      UniProtKB/TrEMBL
      B4E0J2
    2. XM_054343504.1XP_054199479.1  natural resistance-associated macrophage protein 1 isoform X4

      UniProtKB/TrEMBL
      B4E0J2
    3. XM_054343503.1XP_054199478.1  natural resistance-associated macrophage protein 1 isoform X3

      UniProtKB/TrEMBL
      B4DQ73, B9ZVN3
    4. XM_054343505.1XP_054199480.1  natural resistance-associated macrophage protein 1 isoform X5

    5. XM_054343501.1XP_054199476.1  natural resistance-associated macrophage protein 1 isoform X1

      UniProtKB/TrEMBL
      B4E0J2
    6. XM_054343502.1XP_054199477.1  natural resistance-associated macrophage protein 1 isoform X2

      UniProtKB/TrEMBL
      B4E0J2

    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.