Human Gene SLC11A1 (ENST00000354352.9) from GENCODE V44
  Description: solute carrier family 11 member 1 (from HGNC SLC11A1)
RefSeq Summary (NM_000578): 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].
Gencode Transcript: ENST00000354352.9
Gencode Gene: ENSG00000018280.17
Transcript (Including UTRs)
   Position: hg38 chr2:218,382,248-218,395,323 Size: 13,076 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg38 chr2:218,382,369-218,386,659 Size: 4,291 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:218,382,248-218,395,323)mRNA (may differ from genome)Protein (163 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIPubMedUniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SLC11A1
Diseases sorted by gene-association score: buruli ulcer* (599), tuberculosis* (81), typhoid fever (29), tularemia (21), pulmonary tuberculosis (19), leprosy (16), enterobiasis (15), visceral leishmaniasis (15), brucellosis (14), multidrug-resistant tuberculosis (13), salmonellosis (13), crohn's disease (11), nontuberculous mycobacterial lung disease (11), campylobacteriosis (10), diabetes mellitus, insulin-dependent, 12 (9), leishmaniasis (8), diabetes mellitus, insulin-dependent, 13 (8), extrapulmonary tuberculosis (8), diabetes mellitus, insulin-dependent, 7 (8), sarcoidosis 1 (7), post-transplant lymphoproliferative disease (7), cutaneous leishmaniasis (7), mycobacterium avium complex disease (7), primary bacterial infectious disease (6), rheumatoid factor-negative juvenile idiopathic arthritis (5), lymphadenitis (5), rheumatoid arthritis (4), rheumatoid arthritis, systemic juvenile (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 267.55 RPKM in Whole Blood
Total median expression: 600.97 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.00121-0.372 Picture PostScript Text
3' UTR -595.301523-0.391 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001046 - Nat-R-assoc-macro_Nramp

Pfam Domains:
PF01566 - Natural resistance-associated macrophage protein

ModBase Predicted Comparative 3D Structure on Q9HBK0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0046873 metal ion transmembrane transporter activity

Biological Process:
GO:0006955 immune response
GO:0030001 metal ion transport

Cellular Component:
GO:0005575 cellular_component
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK307954 - Homo sapiens cDNA, FLJ97902.
D50402 - Homo sapiens mRNA for NRAMP1, complete cds.
AB209650 - Homo sapiens mRNA for solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 variant protein.
AK310914 - Homo sapiens cDNA, FLJ17956.
AK303398 - Homo sapiens cDNA FLJ54317 complete cds, highly similar to Natural resistance-associated macrophage protein 1.
AK298667 - Homo sapiens cDNA FLJ60324 complete cds, highly similar to Natural resistance-associated macrophage protein 1.
AK311405 - Homo sapiens cDNA, FLJ18447.
D50403 - Homo sapiens mRNA for NRAMP1, complete cds.
AK294707 - Homo sapiens cDNA FLJ53784 complete cds, highly similar to Natural resistance-associated macrophage protein 1.
BC041787 - Homo sapiens solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1, mRNA (cDNA clone IMAGE:4717241), with apparent retained intron.
L32185 - Homo sapiens integral membrane protein (NRAMP1) mRNA, complete cds.
BC071165 - Homo sapiens solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1, mRNA (cDNA clone MGC:90282 IMAGE:5756382), complete cds.
BC033754 - Homo sapiens solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1, mRNA (cDNA clone IMAGE:5212319).
BC037550 - Homo sapiens solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1, mRNA (cDNA clone IMAGE:5213746), with apparent retained intron.
D38171 - Homo sapiens mRNA for Nramp, complete cds.
CU687102 - Synthetic construct Homo sapiens gateway clone IMAGE:100022910 5' read SLC11A1 mRNA.
KJ904563 - Synthetic construct Homo sapiens clone ccsbBroadEn_13957 SLC11A1 gene, encodes complete protein.
JD059600 - Sequence 40624 from Patent EP1572962.
JD488059 - Sequence 469083 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

-  Other Names for This Gene
  Alternate Gene Symbols: B9ZVT9, D50402, ENST00000354352.1, ENST00000354352.2, ENST00000354352.3, ENST00000354352.4, ENST00000354352.5, ENST00000354352.6, ENST00000354352.7, ENST00000354352.8, Q9HBK0, Q9HBK0_HUMAN, uc061sko.1
UCSC ID: ENST00000354352.9
RefSeq Accession: NM_000578
Protein: Q9HBK0

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.