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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

IRGM Gene

protein-coding   GIFtS: 49
GCID: GC05P150208

immunity-related GTPase family, M

(Previous names: immunity-related GTPase family, M1 )
(Previous symbol: IRGM1)
 Explore 11 diseases affiliated with
IRGM via our new
 Human Malady Compendium 
Biological research products
for IRGM
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Immunity-Related GTPase Family, M1 2     Interferon-Inducible Protein 12 3
IFI11 2 3 5     LPS-Stimulated RAW 264.7 Macrophage Protein 47 Homolog2 3
LRG471 2 3 5     Immunity-Related GTPase Family M Protein2
IRGM11 2 3     LRG-47-Like Protein2
LRG-471 2 3     EC 3.6.5.-3
Immunity-Related GTPase Family, M11 2     Immunity-Related GTPase Family M Protein 13

External Ids:    HGNC: 295971   Entrez Gene: 3456112   Ensembl: ENSG000002376937   OMIM: 6082125   UniProtKB: A1A4Y43   

Export aliases for IRGM gene to outside databases

Previous GC identifer: GC05P145371


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for IRGM:
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)

UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4
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)

Gene Wiki entry for IRGM


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.1  NT_029289.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the IRGM gene promoter:
         STAT1   SREBP-1c   STAT1beta   NF-kappaB   STAT1alpha   SREBP-1b   SREBP-1a   POU2F1   POU2F1a   NF-kappaB1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for IRGM

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat IRGM


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q33.1   Ensembl cytogenetic band:  5q33.1   HGNC cytogenetic band: 5q33.1

IRGM Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
IRGM gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P150208:  view genomic region     (about GC identifiers)

Start:
150,226,085 bp from pter      End:
150,280,298 bp from pter
Size:
54,214 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4 (See protein sequence)
Recommended Name: Immunity-related GTPase family M protein  
Size: 181 amino acids; 20142 Da
Subcellular location: Golgi apparatus membrane (By similarity). Cell membrane (By similarity). Cytoplasmic vesicle,
phagosome membrane (By similarity). Cytoplasmic vesicle, autophagosome membrane (By similarity). Cell projection,
phagocytic cup (By similarity). Note=Behaves like an integral membrane protein (By similarity). Recruited to the
plasma membrane around forming phagocytic cups, it remains associated with maturing autophagosomes (By similarity).
Preferentially associated with cis- and medial-Golgi (By similarity)
Miscellaneous: Depletion of IRGM by siRNA favors mycobacteria survival in macrophages
Miscellaneous: 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 (PubMed:16277747)
Sequence caution: Sequence=AAI28169.1; Type=Erroneous initiation; Sequence=EAW61704.1; Type=Erroneous initiation;
Secondary accessions: B3VEX0

Explore the universe of human proteins at neXtProt for IRGM: NX_A1A4Y4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A1A4Y4

  • IRGM Protein expression data from MOPED and PaxDb: --
    REFSEQ proteins: NP_001139277.1  
    ENSEMBL proteins: 
     ENSP00000428220   ENSP00000429819  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for IRGM

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IEA--
    GO:0000421autophagic vacuole membrane IEA--
    GO:0001891phagocytic cup IEA--
    GO:0020003symbiont-containing vacuole ----
    GO:0030670phagocytic vesicle membrane IEA--


    IRGM for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    IRGM for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007743 Interferon-induced_GTPase

    Graphical View of Domain Structure for InterPro Entry A1A4Y4

    ProtoNet protein and cluster: A1A4Y4

    UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4
    Similarity: Belongs to the interferon-inducible GTPase family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4
    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)
    Induction: Not up-regulated by IFNG/IFN-gamma

    Enzyme Number (IUBMB): EC 3.6.5.-1

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    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005525GTP binding IEA--
    GO:0016817hydrolase activity, acting on acid anhydrides IEA--


    IRGM for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Irgm1tm1Gat for IRGM
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Irgm1):
     homeostasis/metabolism  immune system 

    IRGM for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Leishmaniasis
    Toxoplasmosis0.31

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for IRGM):
        Toxoplasmosis


    IRGM for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for IRGM

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006914autophagy IEA--
    GO:0006954inflammatory response IEA--
    GO:0034341response to interferon-gamma ----
    GO:0042742defense response to bacterium ----
    GO:0042832defense response to protozoan ----


    IRGM for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for IRGM
    Search CenterWatch for drugs/clinical trials and news about IRGM 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for IRGM gene: 
    NM_001145805.1  

    Unigene Clusters for IRGM:

    Immunity-related GTPase family, M
    Hs.519680 , Hs.652148  [show with all ESTs]
    Unigene Representative Sequences: BC038539, EU742619
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000522154(uc010jhk.3) ENST00000520549

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    Clone
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    Additional cDNA sequence: 

    BC128167.1 BC128168.1 EU742619.1 

    1 DOTS entry:

    DT.95179447 

    2 AceView cDNA sequences:

    BC038539 BI764111 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    IRGM expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GACCTCAGCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    Genevestigator expression for IRGM

    SOURCE GeneReport for Unigene clusters: Hs.519680 Hs.652148

    UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4
    Tissue specificity: Widely expressed (at protein level). Expressed in several tissues including colon, small bowel and
    peripheral blood leukocytes

        SABiosciences Expression via Pathway-Focused PCR Arrays including IRGM: 
              Interferons & Receptors in human mouse rat
              Nitric Oxide Signaling Pathway in human mouse rat
              Autophagy in human mouse rat
              Cell Death PathwayFinder in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IRGM

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for IRGM gene from 3/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Irgm11 , 5 immunity-related GTPase family M member 11, 5 68.58(n)1
    57.47(a)1
      11 (28.84 cM)5
    159441  NM_008326.11  NP_032352.11 
     488619685 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 5)
    --
    8(a)
    7(a)
    (see all 5)
    possible ortholog
    many → 1
    (see all 5)
    LGf(80022-101229)
    LGf(136835-152301)
    zebrafish
    (Danio rerio)
    Actinopterygii CABZ01079981.16
    CT027800.16
    (see all 10)
    --
    8(a)
    7(a)
    (see all 10)
    many → 1
    many → 1
    (see all 10)
    16(28191446-28193392)
    16(47593699-47598247)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for IRGM gene
    IRGC2  

    IRGM for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/154 NCBI SNPs in IRGM are shown (see all 154    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs796266931,2
    --145370448(+) GATGTA/GTGTAT 1 -- us2k10--------
    rs1143344331,2
    C,F,--145370478(+) CTTAAG/TTATGT 1 -- us2k11Minor allele frequency- T:0.02WA 118
    rs1126358941,2
    --145370809(+) CAGCCC/TGCCGC 1 -- us2k11Minor allele frequency- T:0.50CSA 2
    rs796657551,2
    --145370916(+) GGCTGC/TGGGCG 1 -- us2k13Minor allele frequency- T:0.10CSA NA EA 242
    rs573299401,2
    C,--145370943(+) ACGAGT/ATCCGG 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs1119119171,2
    --145370948(+) TTCCGG/AGTGGG 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1126494241,2
    F,--145370972(+) GGCCCG/ACGCTC 1 -- us2k13Minor allele frequency- A:0.09CSA WA 122
    rs49588461,2
    C,F,H,--145370999(+) cccgaC/Tggccc 1 -- us2k18Minor allele frequency- T:0.50EA NS CSA WA NA 622
    rs77223931,2
    C,--145371932(+) ctgccC/Tgaacc 1 -- us2k10--------
    rs100739521,2
    C,--145372445(+) GAATGC/TAATGA 1 -- ut512Minor allele frequency- T:0.19CSA WA 120

    HapMap Linkage Disequilibrium report for IRGM (150226085 - 150280298 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for IRGM
         3 CNVs: 36358 3580 36357
    Human Gene Mutation Database (HGMD): IRGM

    Locus Specific Mutation Databases (LSDB): IRGM

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    IRGM for disorders           About GeneDecksing

    OMIM gene information: 608212   
    OMIM disorders: 607948  
    UniProtKB/Swiss-Prot: IRGM_HUMAN, A1A4Y4
  • Defects in IRGM are the cause of susceptibility to inflammatory bowel disease type 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

    11 diseases for IRGM:    About MalaCards
    mycobacterium tuberculosis, protection against    tuberculosis, protection against    crohn's disease    tuberculosis
    mycobacterium tuberculosis    ankylosing spondylitis    inflammatory bowel disease    ulcerative colitis
    spondylitis    celiac disease    toxoplasmosis

    3 diseases from the University of Copenhagen DISEASES database for IRGM:
    Crohn's disease     Ulcerative colitis     Tuberculosis
    Human Genome Epidemiology (HuGE) Navigator: IRGM (25 documents)

    Export disorders for IRGM gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for IRGM gene, integrated from 9 sources (see all 51):
    (articles sorted by number of sources associating them with IRGM)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. (PubMed id 19174780)1, 2 Weersma R.K....Vermeire S. (2009)
    2. Death and resurrection of the human IRGM gene. (PubMed id 19266026)1, 2 Bekpen C.... Eichler E.E. (2009)
    3. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. (PubMed id 17554261)1, 2 Parkes M....Mathew C.G. (2007)
    4. Human IRGM induces autophagy to eliminate intracellular mycobacteria. (PubMed id 16888103)1, 2 Singh S.B....Deretic V. (2006)
    5. The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage. (PubMed id 16277747)1, 2 Bekpen C....Howard J.C. (2005)
    6. Immune control of tuberculosis by IFN-gamma-inducible LRG-47. (PubMed id 14576437)1, 3 MacMicking J.D....McKinney J.D. (2003)
    7. Identification of an endotoxin and IFN-inducible cDNA: possible identification of a novel protein family. (PubMed id 7561525)1, 3 Sorace J.M....Drysdale B.E. (1995)
    8. Autophagy gene variant IRGM -261T contributes to prot ection from tuberculosis caused by Mycobacterium tuberculosis but not by M. afr icanum strains. (PubMed id 19750224)1, 9 Intemann C.D....Meyer C.G. (2009)
    9. Mutations in IRGM are associated with more frequent ne ed for surgery in patients with ileocolonic Crohn's disease. (PubMed id 22228152)1 Sehgal R....Koltun W.A. (2012)
    10. IRGM gene polymorphisms and risk of gastric cancer. (PubMed id 22713085)1 Burada F....Saftoiu A. (2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 345611 HGNC: 29597 AceView: LRG47 Ensembl:ENSG00000237693 euGenes: HUgn345611
    ECgene: IRGM Kegg: 345611 H-InvDB: IRGM

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for IRGM Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for IRGM gene:
    Search GeneIP for patents involving IRGM

    GeneCards and IP:
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