Slc11a1 MGI Mouse Gene Detail - MGI:1345275 - solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1

Symbol

Slc11a1
Name

solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1
Synonyms

Bcg, host resistance locus Bcg/Ity/Lsh, ity, Ity, Ity1, Lsh, Nramp, Nramp1

Feature Type

protein coding gene
IDs

MGI:1345275
NCBI Gene: 18173
Alliance

gene page
Transcription Start Sites

18 TSS
Candidate for QTL

1 QTL

Sequence Map

Chr1:74414354-74425221 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 38.54 cM
Mapping Data

64 experiments

SNPs within 2kb

352 from dbSNP Build 142
Strain Annotations

18
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1345275	protein coding gene	Chr1:74414318-74429974 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016149	protein coding gene	Chr1:74972148-74984459 (+)
A/J	MGP_AJ_G0016132	protein coding gene	Chr1:72346983-72358199 (+)
AKR/J	MGP_AKRJ_G0016089	protein coding gene	Chr1:74358815-74369707 (+)
BALB/cJ	MGP_BALBcJ_G0016087	protein coding gene	Chr1:72415486-72426160 (+)
C3H/HeJ	MGP_C3HHeJ_G0015918	protein coding gene	Chr1:74690061-74703154 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0016540	protein coding gene	Chr1:77887287-77899669 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014261	protein coding gene	Chr1:67933715-67944720 (+)
CAST/EiJ	MGP_CASTEiJ_G0015502	protein coding gene	Chr1:74010226-74030576 (+)
CBA/J	MGP_CBAJ_G0015891	protein coding gene	Chr1:80417158-80428663 (+)
DBA/2J	MGP_DBA2J_G0015992	protein coding gene	Chr1:71680560-71691533 (+)
FVB/NJ	MGP_FVBNJ_G0015995	protein coding gene	Chr1:70859327-70870645 (+)
LP/J	MGP_LPJ_G0016064	protein coding gene	Chr1:76076864-76088733 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016015	protein coding gene	Chr1:83831970-83847285 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016587	protein coding gene	Chr1:74425350-74436227 (+)
PWK/PhJ	MGP_PWKPhJ_G0015289	protein coding gene	Chr1:71129737-71142912 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0015067	protein coding gene	Chr1:73792853-73809801 (+)
WSB/EiJ	MGP_WSBEiJ_G0015564	protein coding gene	Chr1:74218426-74231225 (+)

Human Ortholog

SLC11A1, solute carrier family 11 member 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SLC11A1, solute carrier family 11 member 1
Synonyms

LSH, NRAMP, NRAMP1
Links

HGNC:10907

NCBI Gene ID: 6556

neXtProt AC: NX_P49279

UniProt: P49279
Chr Location

2q35; chr2:218382029-218396894 (+) GRCh38

MGI Vertebrate Homology

Slc11a1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SLC11A1
Gene Tree

Slc11a1

Diseases

19 with human SLC11A1 associations

				Human Disease	Mouse Models
				Behcet's disease IDs Behcet's disease DOID:13241 EFO:0003780 ICD10CM:M35.2 ICD9CM:136.1 ICD9CM_2006:136.1 MESH:D001528 NCI:C34416 OMIM:109650 UMLS_CUI:C0004943
				Buruli ulcer disease IDs Buruli ulcer disease DOID:0050456 ICD10CM:A31.1 MESH:D054312 NCI:C84604 UMLS_CUI:C0085568
				Crohn's disease IDs Crohn's disease DOID:8778 DOID:8784 DOID:8855 DOID:8942 EFO:0000384 ICD10CM:K50.1 ICD9CM:555.1 MESH:D003424 NCI:C37262 UMLS_CUI:C0156147
				cutaneous leishmaniasis IDs cutaneous leishmaniasis DOID:9111 DOID:13553 DOID:9110 DOID:9122 DOID:9167 ICD10CM:B55.1 MESH:D016773 NCI:C34768 UMLS_CUI:C0023283
				inflammatory bowel disease IDs inflammatory bowel disease DOID:0050589 EFO:0003767 KEGG:05321 MESH:D015212 NCI:C3138 OMIM:PS266600 UMLS_CUI:C0021390
				juvenile rheumatoid arthritis IDs juvenile rheumatoid arthritis DOID:676 DOID:10129 DOID:1264 DOID:675 ICD10CM:M08.4 ICD9CM:714.3 ICD9CM:714.31 ICD9CM:714.32 ICD9CM:714.33 NCI:C26979 NCI:C61279 OMIM:604302 ORDO:92 UMLS_CUI:C0157916 UMLS_CUI:C0157917 UMLS_CUI:C0157918 UMLS_CUI:C0409667
				leprosy IDs leprosy DOID:1024 EFO:0001054 ICD10CM:A30 ICD9CM:030 ICD9CM:030.9 MESH:D007918 NCI:C84824 OMIM:607572 OMIM:609888 OMIM:613407 ORDO:548 UMLS_CUI:C0023343
				lymphoproliferative syndrome IDs lymphoproliferative syndrome DOID:0060704 OMIM:PS308240 ORDO:538963
				multiple sclerosis IDs multiple sclerosis DOID:2377 ICD10CM:G35 ICD9CM:340 MESH:D009103 NCI:C3243 OMIM:612594 OMIM:612595 OMIM:612596 UMLS_CUI:C0026769
				pulmonary tuberculosis IDs pulmonary tuberculosis DOID:2957 ICD10CM:A15 ICD9CM:011 ICD9CM:011.9 ICD9CM:011.90 MESH:D014397 NCI:C26899 UMLS_CUI:C0041327
				rheumatoid arthritis IDs rheumatoid arthritis DOID:7148 EFO:0000685 ICD10CM:M06.9 ICD9CM:714.0 KEGG:05323 MESH:D001172 NCI:C2884 OMIM:180300 UMLS_CUI:C0003873
				sarcoidosis IDs sarcoidosis DOID:11335 ICD10CM:D86 ICD9CM:135 MESH:D012507 NCI:C34995 ORDO:797 UMLS_CUI:C0036202
				systemic lupus erythematosus IDs systemic lupus erythematosus DOID:9074 ICD10CM:M32.9 ICD9CM:710.0 KEGG:05322 MESH:D008180 NCI:C3201 OMIM:152700 OMIM:300809 OMIM:605480 OMIM:608437 OMIM:609903 OMIM:609939 OMIM:610065 OMIM:610066 OMIM:612254 OMIM:612378 OMIM:613145 OMIM:614420 ORDO:536 UMLS_CUI:C0024141
				systemic scleroderma IDs systemic scleroderma DOID:418 EFO:0000717 ICD10CM:M34.0 ICD9CM_2006:710.1 ICD9CM:710.1 MESH:D012595 NCI:C72070 OMIM:181750 UMLS_CUI:C0036421
				tuberculosis IDs tuberculosis DOID:399 DOID:10096 DOID:12688 DOID:12691 DOID:415 DOID:9901 DOID:9902 MESH:D014375 UMLS_CUI:C0041295
				type 1 diabetes mellitus IDs type 1 diabetes mellitus DOID:9744 ICD10CM:E10 KEGG:04940 MESH:D003922 NCI:C2986 OMIM:222100 UMLS_CUI:C0011854
				ulcerative colitis IDs ulcerative colitis DOID:8577 DOID:8576 DOID:9016 EFO:0000729 ICD10CM:K51 ICD9CM:556 ICD9CM:556.5 ICD9CM:556.9 MESH:D003093 NCI:C2952 UMLS_CUI:C0009324 UMLS_CUI:C0375359
				urinary bladder cancer IDs urinary bladder cancer DOID:11054 DOID:5428 ICD10CM:C67 ICD9CM:188 ICD9CM:188.9 KEGG:05219 MESH:D001749 NCI:C2901 NCI:C9334 OMIM:109800 UMLS_CUI:C0005684 UMLS_CUI:C0005695
				visceral leishmaniasis IDs visceral leishmaniasis DOID:9146 ICD10CM:B55.0 ICD9CM:085.0 MESH:D007898 NCI:C34771 OMIM:608207 OMIM:611381 OMIM:611382 UMLS_CUI:C0023290

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

8 phenotypes from 4 alleles in 8 genetic backgrounds
10 phenotypes from multigenic genotypes
124 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

13
Chemically induced (other)

1
Endonuclease-mediated

4
Radiation induced

1
Spontaneous

1
Targeted

4
Transgenic

1
Genomic Mutations

3 involving Slc11a1
Incidental Mutations

APF
Find Mice (IMSR)

40 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mutations in this gene are associated with susceptibility to infection with pathogens, including Myobacterium, Salmonella and Leishmania. Depending on the mutation, mutants may exhibit either increased or decreased susceptibility to infection.

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All GO Annotations

95
GO References

36

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

753
Tissues

45
cDNA Data

26
Literature Summary

2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase slc11a1

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All Sequences

56
RefSeq

12
UniProt

2
CCDS

CCDS15047.1

Ensembl

ENSMUSG00000026177 (Evidence)
NCBI Gene

18173

			Length	Strain/Species	Flank
genomic	ENSMUSG00000026177	Ensembl Gene Model \| MGI Sequence Detail	10868	C57BL/6J	± kb
transcript	ENSMUST00000027368	Ensembl \| MGI Sequence Detail	2315	Not Applicable
polypeptide	ENSMUSP00000027368	Ensembl \| MGI Sequence Detail	548	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000002994 natural resistance-associated macrophage protein 1

(term hierarchy)
InterPro Domains

IPR001046 NRAMP family
GlyGen

P41251 2 sites

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All nucleic 34

Genomic 6

cDNA 26

Primer pair 2

Microarray probesets 3

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MGD-MRK-11510, MGD-MRK-11511, MGD-MRK-11891, MGD-MRK-1520, MGD-MRK-16714, MGD-MRK-24163, MGI:103283

Summaries

All 244

Developmental Gene Expression 2

Diseases 1

Gene Ontology 36

Phenotypes 124
Earliest

J:24667 Webster LT, Inherited and acquired factors in resistance to infection. I. Development of resistant and susceptible lines of mice through selective breeding. J Exp Med. 1933;57:793-843
Latest

J:346246 Zigdon M, et al., Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1beta. PLoS Biol. 2024 Jan;22(1):e3002486

TSS for Slc11a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr7388	Chr1:74414302-74414331 (+)	-37 bp
Tssr7389	Chr1:74414367-74414388 (+)	24 bp
Tssr7390	Chr1:74414394-74414416 (+)	51 bp
Tssr7391	Chr1:74414417-74414428 (+)	69 bp
Tssr7392	Chr1:74414436-74414448 (+)	88 bp
Tssr7393	Chr1:74414725-74414736 (+)	377 bp
Tssr7394	Chr1:74414742-74414764 (+)	399 bp
Tssr7395	Chr1:74416307-74416318 (+)	1,959 bp
Tssr7396	Chr1:74420060-74420077 (+)	5,715 bp
Tssr7397	Chr1:74420802-74420811 (+)	6,453 bp
Tssr7398	Chr1:74420886-74420895 (+)	6,537 bp
Tssr7399	Chr1:74420901-74420910 (+)	6,552 bp
Tssr7400	Chr1:74420925-74420936 (+)	6,577 bp
Tssr7401	Chr1:74421510-74421523 (+)	7,163 bp
Tssr7402	Chr1:74421526-74421539 (+)	7,179 bp
Tssr7403	Chr1:74421626-74421639 (+)	7,279 bp
Tssr121	Chr1:74424446-74424453 (+)	10,096 bp
Tssr7404	Chr1:74424633-74424668 (+)	10,297 bp

Slc11a1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Idd5.2	Chr1, syntenic		J:107559	Congenic mouse strains within the Idd5.2 (MGI: Idd5b) region of mouse Chromosome 1 were utilized to suggest that solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 (Slc11a1) is a likely candidate for Idd5.2. Using RNAi (RNA interference) the authors showed that a knockdown of Slc11a1 (allele Nramp1) had a detectable effect on diabetes incidence conferred within the Idd5.2 region.

*cM position of peak correlated region/marker

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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