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Aliases for IRGM Gene

Aliases for IRGM Gene

  • Immunity-Related GTPase M 2
  • LPS-Stimulated RAW 264.7 Macrophage Protein 47 Homolog 3 4
  • Immunity-Related GTPase Family, M1 2 3
  • Immunity-Related GTPase Family, M 3 5
  • Interferon-Inducible Protein 1 3 4
  • LRG-47 3 4
  • IRGM1 3 4
  • LRG47 3 4
  • IFI1 3 4
  • Immunity-Related GTPase Family M Protein 1 4
  • LRG-47-Like Protein 3
  • EC 3.6.5.- 4

External Ids for IRGM Gene

Previous HGNC Symbols for IRGM Gene

  • IRGM1

Previous GeneCards Identifiers for IRGM Gene

  • GC05P150208
  • GC05P145371

Summaries for IRGM Gene

Entrez Gene Summary for IRGM Gene

  • This gene encodes a member of the p47 immunity-related GTPase family. The encoded protein may play a role in the innate immune response by regulating autophagy formation in response to intracellular pathogens. Polymorphisms that affect the normal expression of this gene are associated with a susceptibility to Crohn's disease and tuberculosis.[provided by RefSeq, Oct 2010]

GeneCards Summary for IRGM Gene

IRGM (Immunity-Related GTPase M) is a Protein Coding gene. Diseases associated with IRGM include Inflammatory Bowel Disease 19 and Crohn's Disease. Among its related pathways are Toxoplasmosis. GO annotations related to this gene include GTP binding and hydrolase activity, acting on acid anhydrides. An important paralog of this gene is IRGC.

UniProtKB/Swiss-Prot for IRGM Gene

  • Putative GTPase which is required for clearance of acute protozoan and bacterial infections. Functions in innate immune response probably through regulation of autophagy. May regulate proinflammatory cytokine production and prevent endotoxemia upon infection. May also play a role in macrophages adhesion and motility (By similarity).

Gene Wiki entry for IRGM Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IRGM Gene

Genomics for IRGM Gene

Regulatory Elements for IRGM Gene

Enhancers for IRGM Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around IRGM on UCSC Golden Path with GeneCards custom track

Promoters for IRGM Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around IRGM on UCSC Golden Path with GeneCards custom track

Genomic Location for IRGM Gene

Chromosome:
5
Start:
150,846,523 bp from pter
End:
150,902,400 bp from pter
Size:
55,878 bases
Orientation:
Plus strand

Genomic View for IRGM Gene

Genes around IRGM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IRGM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IRGM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IRGM Gene

Proteins for IRGM Gene

  • Protein details for IRGM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A1A4Y4-IRGM_HUMAN
    Recommended name:
    Immunity-related GTPase family M protein
    Protein Accession:
    A1A4Y4
    Secondary Accessions:
    • B3VEX0

    Protein attributes for IRGM Gene

    Size:
    181 amino acids
    Molecular mass:
    20142 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Depletion of IRGM by siRNA favors mycobacteria survival in macrophages.
    • There is a huge difference in terms of sequence and regulation of expression compared to the mouse ortholog and hence, the function might be slightly different.
    SequenceCaution:
    • Sequence=AAI28169.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=EAW61704.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for IRGM Gene

Proteomics data for IRGM Gene at MOPED

Post-translational modifications for IRGM Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for IRGM Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for IRGM

No data available for DME Specific Peptides for IRGM Gene

Domains & Families for IRGM Gene

Protein Domains for IRGM Gene

Suggested Antigen Peptide Sequences for IRGM Gene

Graphical View of Domain Structure for InterPro Entry

A1A4Y4

UniProtKB/Swiss-Prot:

IRGM_HUMAN :
  • The G5 motif of the IRG-type G domain is missing because the IRGM protein is truncated in anthropoids.
  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. IRG family.
Domain:
  • The G5 motif of the IRG-type G domain is missing because the IRGM protein is truncated in anthropoids.
  • Contains 1 IRG-type G (guanine nucleotide-binding) domain.
Family:
  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. IRG family.
genes like me logo Genes that share domains with IRGM: view

No data available for Gene Families for IRGM Gene

Function for IRGM Gene

Molecular function for IRGM Gene

UniProtKB/Swiss-Prot Function:
Putative GTPase which is required for clearance of acute protozoan and bacterial infections. Functions in innate immune response probably through regulation of autophagy. May regulate proinflammatory cytokine production and prevent endotoxemia upon infection. May also play a role in macrophages adhesion and motility (By similarity).
UniProtKB/Swiss-Prot Induction:
Not up-regulated by IFNG/IFN-gamma.

Enzyme Numbers (IUBMB) for IRGM Gene

Phenotypes for IRGM Gene

genes like me logo Genes that share phenotypes with IRGM: view

Human Phenotype Ontology for IRGM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

No data available for Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for IRGM Gene

Localization for IRGM Gene

Subcellular locations from UniProtKB/Swiss-Prot for IRGM Gene

Golgi apparatus membrane. Cell membrane. Cytoplasmic vesicle, phagosome membrane. Cytoplasmic vesicle, autophagosome membrane. Cell projection, phagocytic cup. Note=Behaves like an integral membrane protein. Recruited to the plasma membrane around forming phagocytic cups, it remains associated with maturing autophagosomes. Preferentially associated with cis- and medial-Golgi. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for IRGM Gene COMPARTMENTS Subcellular localization image for IRGM gene
Compartment Confidence
vacuole 4
golgi apparatus 3
plasma membrane 3
cytosol 2
extracellular 2
nucleus 2
cytoskeleton 1
lysosome 1

Gene Ontology (GO) - Cellular Components for IRGM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000421 autophagosome membrane IEA --
GO:0030670 phagocytic vesicle membrane IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with IRGM: view

Pathways & Interactions for IRGM Gene

SuperPathways for IRGM Gene

Superpath Contained pathways
1 Toxoplasmosis
genes like me logo Genes that share pathways with IRGM: view

Pathways by source for IRGM Gene

1 KEGG pathway for IRGM Gene

Interacting Proteins for IRGM Gene

Gene Ontology (GO) - Biological Process for IRGM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
genes like me logo Genes that share ontologies with IRGM: view

No data available for SIGNOR curated interactions for IRGM Gene

Drugs & Compounds for IRGM Gene

No Compound Related Data Available

Transcripts for IRGM Gene

mRNA/cDNA for IRGM Gene

(2) REFSEQ mRNAs :
(2) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for IRGM Gene

No ASD Table

Relevant External Links for IRGM Gene

GeneLoc Exon Structure for
IRGM
ECgene alternative splicing isoforms for
IRGM

Expression for IRGM Gene

mRNA expression in normal human tissues for IRGM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IRGM Gene

This gene is overexpressed in Whole Blood (x5.1).

SOURCE GeneReport for Unigene cluster for IRGM Gene Hs.519680

mRNA Expression by UniProt/SwissProt for IRGM Gene

A1A4Y4-IRGM_HUMAN
Tissue specificity: Widely expressed (at protein level). Expressed in several tissues including colon, small bowel and peripheral blood leukocytes.
genes like me logo Genes that share expression patterns with IRGM: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for IRGM Gene

Orthologs for IRGM Gene

This gene was present in the common ancestor of chordates.

Orthologs for IRGM Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia IRGM 35
  • 72.66 (n)
  • 60.11 (a)
-- 36
  • 24 (a)
OneToMany
IFGGD3 36
  • 21 (a)
OneToMany
IRGM5 36
  • 24 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Irgm2 35
  • 68.74 (n)
  • 54.8 (a)
Irgm2 16
Igtp 36
  • 21 (a)
OneToMany
Irgm1 36
  • 23 (a)
OneToMany
Irgm2 36
  • 23 (a)
OneToMany
chimpanzee
(Pan troglodytes)
Mammalia IRGM 35
  • 98.34 (n)
  • 96.69 (a)
IRGM 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Irgm2 35
  • 70.64 (n)
  • 55.68 (a)
cow
(Bos Taurus)
Mammalia IFI47 36
  • 16 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia IRGM 36
  • 17 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 25 (a)
OneToMany
-- 36
  • 8 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia IRGM 36
  • 12 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii CT027800.1 36
  • 5 (a)
ManyToMany
irgf3 36
  • 15 (a)
ManyToMany
irgq1 36
  • 9 (a)
ManyToMany
irgq2 36
  • 10 (a)
ManyToMany
Species with no ortholog for IRGM:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for IRGM Gene

ENSEMBL:
Gene Tree for IRGM (if available)
TreeFam:
Gene Tree for IRGM (if available)

Paralogs for IRGM Gene

Paralogs for IRGM Gene

(1) SIMAP similar genes for IRGM Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with IRGM: view

Variants for IRGM Gene

Sequence variations from dbSNP and Humsavar for IRGM Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs180802994 - 150,848,174(+) CCAGA(A/C/G)GTGAT reference, missense
rs72553867 - 150,848,404(+) TGGCA(A/C)AGGGT reference, missense
rs751627 -- 150,845,551(-) CTGAG(C/T)GCGGG upstream-variant-2KB
rs2880791 -- 150,887,814(-) agtta(G/T)cactc intron-variant
rs2880792 -- 150,873,107(-) catta(C/T)ggtag intron-variant

Structural Variations from Database of Genomic Variants (DGV) for IRGM Gene

Variant ID Type Subtype PubMed ID
dgv1862e1 CNV Complex 17122850
nsv428129 CNV Loss 18775914
dgv1863e1 CNV Complex 17122850
nsv5067 CNV Loss 18451855
nsv883032 CNV Loss 21882294

Variation tolerance for IRGM Gene

Gene Damage Index Score: 3.58; 56.15% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for IRGM Gene

Human Gene Mutation Database (HGMD)
IRGM

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IRGM Gene

Disorders for IRGM Gene

MalaCards: The human disease database

(5) MalaCards diseases for IRGM Gene - From: OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
inflammatory bowel disease 19
  • ibd19
crohn's disease
  • ileitis
ulcerative colitis
  • left-sided ulcerative colitis
colitis
intestinal disease
  • intestinal diseases
- elite association - COSMIC cancer census association via MalaCards
Search IRGM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

IRGM_HUMAN
  • Inflammatory bowel disease 19 (IBD19) [MIM:612278]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269 PubMed:17554261, ECO:0000269 PubMed:19174780, ECO:0000269 PubMed:21278745}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for IRGM

Genetic Association Database (GAD)
IRGM
Human Genome Epidemiology (HuGE) Navigator
IRGM
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
IRGM
genes like me logo Genes that share disorders with IRGM: view

No data available for Genatlas for IRGM Gene

Publications for IRGM Gene

  1. Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. (PMID: 19174780) Weersma R.K. … Vermeire S. (Am. J. Gastroenterol. 2009) 3 4 48 67
  2. Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains. (PMID: 19750224) Intemann C.D. … Meyer C.G. (PLoS Pathog. 2009) 3 23
  3. Immune control of tuberculosis by IFN-gamma-inducible LRG-47. (PMID: 14576437) MacMicking J.D. … McKinney J.D. (Science 2003) 2 3
  4. Identification of an endotoxin and IFN-inducible cDNA: possible identification of a novel protein family. (PMID: 7561525) Sorace J.M. … Drysdale B.E. (J. Leukoc. Biol. 1995) 2 3
  5. IFNg-induced Irgm1 promotes tumorigenesis of melanoma via dual regulation of apoptosis and Bif-1-dependent autophagy. (PMID: 25619828) Dong H. … Xu H. (Oncogene 2015) 3

Products for IRGM Gene

Sources for IRGM Gene

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