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IRF1 Gene

protein-coding   GIFtS: 69
GCID: GC05M131817

Interferon Regulatory Factor 1

Microbiology & Infectious Diseases Congress
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Interferon Regulatory Factor 11 2
IRF-12 3
MAR2 5
Interferon Regulatory Factor-11
Interferon Regulatory Factor 1 Isoform D782

External Ids:    HGNC: 61161   Entrez Gene: 36592   Ensembl: ENSG000001253477   OMIM: 1475755   UniProtKB: P109143   

Export aliases for IRF1 gene to outside databases

Previous GC identifers: GC05M131340 GC05M132265 GC05M131849 GC05M131894 GC05M131846 GC05M127009


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for IRF1 Gene:
IRF1 encodes interferon regulatory factor 1, a member of the interferon regulatory transcription factor (IRF)
family. IRF1 serves as an activator of interferons alpha and beta transcription, and in mouse it has been shown
to be required for double-stranded RNA induction of these genes. IRF1 also functions as a transcription activator
of genes induced by interferons alpha, beta, and gamma. Further, IRF1 has been shown to play roles in regulating
apoptosis and tumor-suppressoion. (provided by RefSeq, Jul 2008)

GeneCards Summary for IRF1 Gene:
IRF1 (interferon regulatory factor 1) is a protein-coding gene. Diseases associated with IRF1 include myelodysplastic syndrome, preleukemic, and nonsmall cell lung cancer, somatic. GO annotations related to this gene include RNA polymerase II core promoter proximal region sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is IRF8.

UniProtKB/Swiss-Prot: IRF1_HUMAN, P10914
Function: Transcriptional regulator which displays a remarkable functional diversity in the regulation of cellular
responses. These include the regulation of IFN and IFN-inducible genes, host response to viral and bacterial
infections, regulation of many genes expressed during hematopoiesis, inflammation, immune responses and cell
proliferation and differentiation, regulation of the cell cycle and induction of growth arrest and programmed
cell death following DNA damage. Stimulates both innate and acquired immune responses through the activation of
specific target genes and can act as a transcriptional activator and repressor regulating target genes by binding
to an interferon-stimulated response element (ISRE) in their promoters. Its target genes for transcriptional
activation activity include: genes involved in anti-viral response, such as IFN-alpha/beta, DDX58/RIG-I,
TNFSF10/TRAIL, OAS1/2, PIAS1/GBP, EIF2AK2/PKR and RSAD2/viperin; antibacterial response, such as NOS2/INOS;
anti-proliferative response, such as p53/TP53, LOX and CDKN1A; apoptosis, such as BBC3/PUMA, CASP1, CASP7 and
CASP8; immune response, such as IL7, IL12A/B and IL15, PTGS2/COX2 and CYBB; DNA damage responses and DNA repair,
such as POLQ/POLH; MHC class I expression, such as TAP1, PSMB9/LMP2, PSME1/PA28A, PSME2/PA28B and B2M and MHC
class II expression, such as CIITA. Represses genes involved in anti-proliferative response, such as
BIRC5/survivin, CCNB1, CCNE1, CDK1, CDK2 and CDK4 and in immune response, such as FOXP3, IL4, ANXA2 and TLR4.
Stimulates p53/TP53-dependent transcription through enhanced recruitment of EP300 leading to increased
acetylation of p53/TP53. Plays an important role in immune response directly affecting NK maturation and
activity, macrophage production of IL12, Th1 development and maturation of CD8+ T-cells. Also implicated in the
differentiation and maturation of dendritic cells and in the suppression of regulatory T (Treg) cells
development. Acts as a tumor suppressor and plays a role not only in antagonism of tumor cell growth but also in
stimulating an immune response against tumor cells

Gene Wiki entry for IRF1 Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000005.10  NT_034772.7  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the IRF1 gene promoter:
         STAT1   IRF-7A   STAT1beta   C/EBPalpha   STAT1alpha   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidIRF1 promoter sequence
   Search Chromatin IP Primers for IRF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat IRF1


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

Entrez Gene cytogenetic band: 5q31.1   Ensembl cytogenetic band:  5q31.1   HGNC cytogenetic band: 5q23-q31

IRF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
IRF1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M131817:  view genomic region     (about GC identifiers)

Start:
131,817,301 bp from pter      End:
131,826,490 bp from pter
Size:
9,190 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: IRF1_HUMAN, P10914 (See protein sequence)
Recommended Name: Interferon regulatory factor 1  
Size: 325 amino acids; 36502 Da
Subunit: Monomer. Homodimer. Interacts with MYD88 and PIAS3 (By similarity). Interacts with EP300
Miscellaneous: Deletion or rearrangement of IRF1 are found in preleukemic myelodysplastic syndrome (MDS) and acute
myelogenous leukemia (AML)
Secondary accessions: Q96GG7

Explore the universe of human proteins at neXtProt for IRF1: NX_P10914

Explore proteomics data for IRF1 at MOPED

Post-translational modifications: 

  • Phosphorylated by CK2 and this positively regulates its activity1
  • Sumoylation represses the transcriptional activity and displays enhanced resistance to protein degradation.
    Inactivates the tumor suppressor activity. Elevated levels in tumor cells. Major site is Lys-275. Sumoylation is
    enhanced by PIAS3 (By similarity). Desumoylated by SENP1 in tumor cells and appears to compete with
    ubiquitination on C-terminal sites1
  • Ubiquitinated. Appears to compete with sumoylation on C-terminal sites1
  • Ubiquitination2 at Lys50, Lys299
  • Modification sites at PhosphoSitePlus

  • See IRF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002189.1  
    ENSEMBL proteins: 
     ENSP00000245414   ENSP00000384406   ENSP00000405655   ENSP00000396318   ENSP00000392455  
     ENSP00000473661  
    Reactome Protein details: P10914

    IRF1 Human Recombinant Protein Products:

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    OriGene Custom MassSpec
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    Novus Biologicals IRF1 Proteins
    Novus Biologicals IRF1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for IRF1
    Cloud-Clone Corp. Proteins for IRF1

    IRF1 Antibody Products:

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    Abcam antibodies for IRF1
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    LSBio Antibodies in human, mouse, rat for IRF1

    IRF1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for IRF1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for IRF1
    Cloud-Clone Corp. CLIAs for IRF1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR001346 Interferon_reg_fact_DNA-bd_dom
     IPR019817 Interferon_reg_fac_CS
     IPR017431 Interferon_reg_fac-1/2
     IPR011991 WHTH_DNA-bd_dom

    Graphical View of Domain Structure for InterPro Entry P10914

    ProtoNet protein and cluster: P10914

    1 Blocks protein domain: IPB001346 Interferon regulatory factor

    UniProtKB/Swiss-Prot: IRF1_HUMAN, P10914
    Similarity: Belongs to the IRF family
    Similarity: Contains 1 IRF tryptophan pentad repeat DNA-binding domain


    IRF1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: IRF1_HUMAN, P10914
    Function: Transcriptional regulator which displays a remarkable functional diversity in the regulation of cellular
    responses. These include the regulation of IFN and IFN-inducible genes, host response to viral and bacterial
    infections, regulation of many genes expressed during hematopoiesis, inflammation, immune responses and cell
    proliferation and differentiation, regulation of the cell cycle and induction of growth arrest and programmed
    cell death following DNA damage. Stimulates both innate and acquired immune responses through the activation of
    specific target genes and can act as a transcriptional activator and repressor regulating target genes by binding
    to an interferon-stimulated response element (ISRE) in their promoters. Its target genes for transcriptional
    activation activity include: genes involved in anti-viral response, such as IFN-alpha/beta, DDX58/RIG-I,
    TNFSF10/TRAIL, OAS1/2, PIAS1/GBP, EIF2AK2/PKR and RSAD2/viperin; antibacterial response, such as NOS2/INOS;
    anti-proliferative response, such as p53/TP53, LOX and CDKN1A; apoptosis, such as BBC3/PUMA, CASP1, CASP7 and
    CASP8; immune response, such as IL7, IL12A/B and IL15, PTGS2/COX2 and CYBB; DNA damage responses and DNA repair,
    such as POLQ/POLH; MHC class I expression, such as TAP1, PSMB9/LMP2, PSME1/PA28A, PSME2/PA28B and B2M and MHC
    class II expression, such as CIITA. Represses genes involved in anti-proliferative response, such as
    BIRC5/survivin, CCNB1, CCNE1, CDK1, CDK2 and CDK4 and in immune response, such as FOXP3, IL4, ANXA2 and TLR4.
    Stimulates p53/TP53-dependent transcription through enhanced recruitment of EP300 leading to increased
    acetylation of p53/TP53. Plays an important role in immune response directly affecting NK maturation and
    activity, macrophage production of IL12, Th1 development and maturation of CD8+ T-cells. Also implicated in the
    differentiation and maturation of dendritic cells and in the suppression of regulatory T (Treg) cells
    development. Acts as a tumor suppressor and plays a role not only in antagonism of tumor cell growth but also in
    stimulating an immune response against tumor cells
    Enzyme regulation: Activated by MYD88 (By similarity)
    Induction: By viruses and interferon (IFN)

         Genatlas biochemistry entry for IRF1:
    interferon regulatory factor 1,transcriptional activator for IFNA,IFNB and IFN-stimulated genes,a modulator of
    virus-induced signaling,antioncogene deleted in MDS,AML,differentiated gastric adenocarcinomas (see TSG5D),tumor
    suppressor transcription factor inducing apoptosis of tumorigenic cell lines

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000975regulatory region DNA binding ----
    GO:0000978RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA18035482
    GO:0003677DNA binding TAS11846971
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0005515protein binding IPI10702232
         
    IRF1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for IRF1:
     Elongated cells  Enable proliferation in B-Raf   Increased cell death HMECs cel 

         11 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Irf1):
     cardiovascular system  cellular  hematopoietic system  homeostasis/metabolism  immune system 
     integument  mortality/aging  normal  renal/urinary system  skeleton 
     tumorigenesis 

    IRF1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for IRF1: Irf1tm1Mak Irf1tm1Cwe

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for IRF1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for IRF1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for IRF1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for IRF1

    Transcription Factor Targeting: 
    Selected GeneGlobe predicted Target genes for IRF1 (see all 489):
    ACAA1,  ACRBP,  ACTRT2,  ACVR1B,  ACYP1,  ADAM17,  ADAM8,  AGPAT4,  AGTR2,  AKAP11

    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  GAAAGTGAAAGT 

    miRNA
    Products:
        
    miRTarBase miRNAs that target IRF1:
    hsa-mir-93-5p (MIRT027994), hsa-mir-383-5p (MIRT006535), hsa-mir-296-3p (MIRT038441)

    Block miRNA regulation of human, mouse, rat IRF1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate IRF1 (see all 81):
    hsa-miR-548j hsa-miR-3678-3p hsa-miR-642a hsa-miR-3194-5p hsa-miR-106a hsa-miR-342-3p hsa-miR-3122 hsa-miR-383
    SwitchGear 3'UTR luciferase reporter plasmidIRF1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for IRF1
    Predesigned siRNA for gene silencing in human, mouse, rat IRF1

    Gene Editing
    Products:
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    Clone
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    GenScript: all cDNA clones in your preferred vector: IRF1 (NM_002198)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for IRF1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat IRF1

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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IRF1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    IRF1_HUMAN, P10914: Nucleus. Cytoplasm. Note=MYD88-associated IRF1 migrates into the nucleus more efficiently
    than non-MYD88-associated IRF1
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    extracellular2
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000790nuclear chromatin IDA18035482
    GO:0005634nucleus TAS11846971
    GO:0005654nucleoplasm TAS--
    GO:0005737cytoplasm ISS--
    GO:0005829cytosol TAS--

    IRF1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for IRF1 About   (see all 22)  
    See pathways by source

    SuperPathContained pathways About
    1Prolactin Signaling Pathway
    Development Prolactin receptor signaling0.39
    Prolactin signaling pathway0.33
    Prolactin Signaling Pathway0.39
    2Immune response IFN alpha beta signaling pathway
    Immune response IFN alpha beta signaling pathway0.69
    Interferon alpha/beta signaling0.43
    3Immune response IFN gamma signaling pathway
    IFN-gamma pathway0.43
    Immune response IFN gamma signaling pathway0.43
    4Interferon Signaling
    Interferon Signaling0.59
    Interferon gamma signaling0.41
    Cytokine Signaling in Immune system0.59
    5Immune response Bacterial infections in normal airways
    Immune response Bacterial infections in normal airways0.78
    Bacterial infections in CF airways0.78

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for IRF1
        iNOS Signaling

    1 Cell Signaling Technology (CST) Pathway for IRF1
        NF-kappaB Signaling

    Selected GeneGo (Thomson Reuters) Pathways for IRF1 (see all 7)
        Immune response Bacterial infections in normal airways
    Development Prolactin receptor signaling
    Immune response IL-12 signaling pathway
    Immune response IFN gamma signaling pathway
    Bacterial infections in CF airways

    Selected BioSystems Pathways for IRF1 (see all 10)
        Apoptosis
    Senescence and Autophagy
    Type II interferon signaling (IFNG)
    IL-7 Signaling Pathway
    Prolactin Signaling Pathway

    4 Reactome Pathways for IRF1
        Interferon alpha/beta signaling
    Interferon gamma signaling
    Factors involved in megakaryocyte development and platelet production
    TRAF6 mediated IRF7 activation


    3 Kegg Pathways  (Kegg details for IRF1):
        Prolactin signaling pathway
    Pertussis
    Hepatitis C


    IRF1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including IRF1 (see all 13): 
              HIV Host Response in human mouse rat
              NFKB Signaling Targets in human mouse rat
              Interferons & Receptors in human mouse rat
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Inflammasomes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for IRF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for IRF1 (P109141, 2, 3 ENSP000002454144) via UniProtKB, MINT, STRING, and/or I2D (see all 116)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IRF8Q025563, ENSP000002686384I2D: score=5 STRING: ENSP00000268638
    RELAQ042063, ENSP000003842734I2D: score=4 STRING: ENSP00000384273
    STAT1P422243, ENSP000003543944I2D: score=4 STRING: ENSP00000354394
    HMGA1P170963, ENSP000003082274I2D: score=3 STRING: ENSP00000308227
    NFKB1P198383, ENSP000002265744I2D: score=3 STRING: ENSP00000226574
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 25):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002819regulation of adaptive immune response TAS11846971
    GO:0006366transcription from RNA polymerase II promoter TAS2475256
    GO:0006915apoptotic process IDA19851330
    GO:0007050cell cycle arrest IDA--
    GO:0007596blood coagulation TAS--

    IRF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for IRF1

    Selected Novoseek inferred chemical compound relationships for IRF1 gene (see all 44)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    2',5'-oligoadenylate 70.4 9 15516717 (1), 8704165 (1), 8265581 (1), 10074208 (1) (see all 8)
    ifn-alpha 66.8 15 17617740 (2), 15077162 (1), 12967644 (1), 20457620 (1) (see all 8)
    indoleamine 63 5 16672265 (2), 15494045 (1), 8663541 (1)
    am 580 51.7 6 16636311 (2), 16085646 (1)
    retinoic acid 47.7 78 8704165 (6), 12204966 (5), 16636311 (5), 16085646 (5) (see all 22)
    poly(i-c) 44.5 3 8027591 (2), 9858321 (1)
    tyrosine 39.6 18 11483597 (4), 9092512 (2), 11804954 (2), 10404396 (1) (see all 8)
    rantes 38 10 16707500 (3), 11390609 (2), 10713367 (1), 12165487 (1) (see all 6)
    pdtc 36.7 3 11739238 (1), 16284791 (1), 12704788 (1)
    polyinosinic-polycytidylic acid 36.2 1 1371248 (1)



    IRF1 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for IRF1 gene: 
    NM_002198.2  

    Unigene Cluster for IRF1:

    Interferon regulatory factor 1
    Hs.436061  [show with all ESTs]
    Unigene Representative Sequence: NM_002198
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000245414(uc003kxa.2 uc003kxb.2) ENST00000472045 ENST00000405885(uc010jdt.2)
    ENST00000437654(uc003kxd.2) ENST00000459982 ENST00000458069 ENST00000463784
    ENST00000439555 ENST00000476613 ENST00000493208
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate IRF1 (see all 81):
    hsa-miR-548j hsa-miR-3678-3p hsa-miR-642a hsa-miR-3194-5p hsa-miR-106a hsa-miR-342-3p hsa-miR-3122 hsa-miR-383
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    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: IRF1 (NM_002198)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat IRF1
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat IRF1
      QuantiFast Probe-based Assays in human, mouse, rat IRF1

    Additional mRNA sequence: 

    AB103081.1 AK314025.1 BC009483.2 BT019755.1 BT019756.1 CR541713.1 X14454.1 

    11 DOTS entries:

    DT.206801  DT.456117  DT.95103231  DT.95335564  DT.120846032  DT.120846289  DT.95188797  DT.100787015 
    DT.120846039  DT.95272124  DT.95272134 

    Selected AceView cDNA sequences (see all 351):

    BQ052012 BX112710 BG756010 AW167090 BF974277 BQ710237 BG754246 BG684240 
    BQ052814 CR594837 BM767147 BX335394 BM747007 BI962874 BX099146 BQ054218 
    BQ949894 CD368134 BQ960301 BI822732 BI771693 BM782704 BG924491 BQ052358 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for IRF1 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b
    SP1:                                -     -                                               -                 -                           
    SP2:                          -     -     -                                               -                 -                           
    SP3:                                -     -                                               -     -                                       
    SP4:                                -     -                                               -                                             
    SP5:                                -                                                                                                   


    ECgene alternative splicing isoforms for IRF1

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    IRF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTGAACACA
    IRF1 Expression
    About this image


    IRF1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 13) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
     
     Neural Crest (Gastrulation Derivatives)
             PureStem SM30, NCr-fac & Meso-latp Progenitor
     
     Epithelial Cells
             Duct Cells Pancreatic Ducts
     
     Bone (Muscoskeletal System)
             Bone Marrow
    IRF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    IRF1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.436061
        Pathway & Disease-focused RT2 Profiler PCR Arrays including IRF1 (see all 13): 
              HIV Host Response in human mouse rat
              NFKB Signaling Targets in human mouse rat
              Interferons & Receptors in human mouse rat
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Inflammasomes in human mouse rat

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IRF1

    (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

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    This gene was present in the common ancestor of chordates.

    Orthologs for IRF1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Irf11 , 5 interferon regulatory factor 11, 5 84.51(n)1
    85.54(a)1
      11 (32.00 cM)5
    163621  NM_001159396.11  NP_001152868.11 
     537700145 
    chicken
    (Gallus gallus)
    Aves IRF11 interferon regulatory factor 1 69.27(n)
    64.17(a)
      396384  NM_205415.1  NP_990746.1 
    lizard
    (Anolis carolinensis)
    Reptilia IRF16
    interferon regulatory factor 1
    49(a)
    1 ↔ 1
    2(127733544-127773599)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC686912 hypothetical protein MGC68691 74.53(n)    BC059984.1 
    zebrafish
    (Danio rerio)
    Actinopterygii AY398364.12   -- 75.91(n)    AY398364.1 


    ENSEMBL Gene Tree for IRF1 (if available)
    TreeFam Gene Tree for IRF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for IRF1 gene
    IRF82  IRF22  IRF52  IRF32  IRF42  IRF92  IRF72  IRF62  
    6 SIMAP similar genes for IRF1 using alignment to 9 protein entries:     IRF1_HUMAN (see all proteins):
    IRF2    IRF4    IRF8    IRF9    IRF5    IRF3

    IRF1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for IRF1 (see all 274)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0651354
    Gastric cancer (GASC)4--see VAR_0651352 W R mis40--------
    VAR_0651344
    Gastric cancer (GASC)4--see VAR_0651342 M L mis40--------
    rs342722521,2
    C--131817748(+) TTTTTT/-GAGAC 1 -- ut311Minor allele frequency- -:0.50CSA 2
    rs343291421,2
    C--131817912(+) TTTTT-/T/TTTT
            
    GAGAC
    2 -- ut31 cds11NA 2
    rs559595571,2
    C--131818356(+) TTTTT-/T/    
       TTTTT
    GGTGC
    2 -- ut311NA 2
    rs58714551,2
    C--131818771(+) CCACA-/CCCCTT 1 -- ut312Minor allele frequency- C:0.00NA CSA 4
    rs113479831,2
    C--131818829(+) CGTCC-/TTATGT 1 -- ut310--------
    rs1422443611,2
    C--131821520(+) CTCTG-/ACGACAC 1 -- int10--------
    rs721267801,2
    C--131821521(+) TCTGA-/ACCACAC 1 -- int10--------
    rs1119066391,2
    C--131821541(+) ACACA-/C/CACACACA
    C
    /CACACACACAC
    CCCTC
    2 -- int1 cds11CSA 2

    HapMap Linkage Disequilibrium report for IRF1 (131817301 - 131826490 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for IRF1: --
    Human Gene Mutation Database (HGMD): IRF1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing IRF1
    DNA2.0 Custom Variant and Variant Library Synthesis for IRF1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 147575   
    OMIM disorders: 613659  211980  
    UniProtKB/Swiss-Prot: IRF1_HUMAN, P10914
  • Gastric cancer (GASC) [MIM:613659]: A malignant disease which starts in the stomach, can spread to the
    esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It
    also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to
    adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types
    are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated
    infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually
    exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in
    sporadic disease. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for IRF1 (see all 99):    
    About MalaCards
    myelodysplastic syndrome, preleukemic    nonsmall cell lung cancer, somatic    mumps    gastric cancer, somatic
    newcastle disease    subacute sclerosing panencephalitis    hereditary diffuse gastric cancer    diffuse gastric cancer
    acute myeloid leukemia, adult    5q- syndrome    measles    celiac disease
    gonadoblastoma    atopy    myocarditis    familial adenomatous polyposis
    acute graft versus host disease    bullous pemphigoid    neuroendocrine carcinoma    smallpox

    1 disease from the University of Copenhagen DISEASES database for IRF1:
    Cancer

    IRF1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    Selected Novoseek inferred disease relationships for IRF1 gene (see all 76)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tumors 47.2 150 15149633 (5), 11323500 (4), 16241857 (4), 15241475 (3) (see all 72)
    necrosis 44.3 17 14708625 (3), 9251759 (2), 14729660 (1), 11096458 (1) (see all 12)
    virus infection 43.6 16 10094406 (1), 15378396 (1), 9251759 (1), 11904369 (1) (see all 13)
    leukemia promyelocytic acute 39.5 3 10602416 (2), 16914093 (1)
    myelodysplastic syndromes 38.9 10 9315094 (1), 10807049 (1), 8809574 (1), 12358902 (1) (see all 6)
    hematopoietic malignancies 31.4 5 7687740 (1), 8625321 (1), 7936656 (1), 9865486 (1)
    leukemogenesis 30.4 3 10921095 (1), 10609788 (1)
    inflammation 30.4 18 19443641 (3), 10498899 (2), 17532542 (1), 12677441 (1) (see all 10)
    leukemia 29.6 26 10921095 (3), 8438156 (3), 8622878 (3), 8809574 (2) (see all 14)
    fanconis anemia 25.8 2 19129219 (1)

    Genetic Association Database (GAD): IRF1
    Human Genome Epidemiology (HuGE) Navigator: IRF1 (48 documents)

    Export disorders for IRF1 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)
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    PubMed articles for IRF1 gene, integrated from 10 sources (see all 682):
    (articles sorted by number of sources associating them with IRF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sequence of a cDNA coding for human IRF-1. (PubMed id 2726461)1, 2, 3 Maruyama M.... Taniguchi T. (Nucleic Acids Res. 1989)
    2. A role for casein kinase II phosphorylation in the regulation of IRF- 1 transcriptional activity. (PubMed id 10094406)1, 2, 9 Lin R. and Hiscott J. (Mol. Cell. Biochem. 1999)
    3. Mutation screening of interferon regulatory factor 1 gene (IRF-1) as a candidate gene for atopy/asthma. (PubMed id 11069564)1, 4, 9 Noguchi E....Hamaguchi H. (Clin. Exp. Allergy 2000)
    4. Interferon regulatory factor 1 binding to p300 stimulates DNA- dependent acetylation of p53. (PubMed id 15509808)1, 2, 9 Dornan D....Ball K.L. (Mol. Cell. Biol. 2004)
    5. Central role of interferon regulatory factor-1 (IRF-1) in controlling retinoic acid inducible gene-I (RIG-I) expression. (PubMed id 17516545)1, 2, 9 Su Z.Z.... Fisher P.B. (J. Cell. Physiol. 2007)
    6. No evidence for genetic association of interferon regulatory factor 1 in juvenile idiopathic arthritis. (PubMed id 17328074)1, 4, 9 Fife M.S....Woo P. (Arthritis Rheum. 2007)
    7. Human interferon regulatory factor 1: intron-exon organization. (PubMed id 1382447)1, 2, 9 Cha Y.... Deisseroth A.B. (DNA Cell Biol. 1992)
    8. Association of interferon-gamma and interferon regulatory factor 1 polymorphisms with asthma in a family-based association study in Taiwan. (PubMed id 16961714)1, 4, 9 Wang T.N....Ko Y.C. (Clin. Exp. Allergy 2006)
    9. Functionally inactivating point mutation in the tumor-suppressor IRF- 1 gene identified in human gastric cancer. (PubMed id 9679752)1, 2, 9 Nozawa H.... Tanaka N. (Int. J. Cancer 1998)
    10. Type I interferons and interferon regulatory factors regulate TNF- related apoptosis-inducing ligand (TRAIL) in HIV-1-infected macrophages. (PubMed id 19404407)1, 2, 9 Huang Y.... Zheng J.C. (PLoS ONE 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3659 HGNC: 6116 AceView: IRF1 Ensembl:ENSG00000125347 euGenes: HUgn3659
    ECgene: IRF1 Kegg: 3659 H-InvDB: IRF1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for IRF1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for IRF1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for IRF1 gene:
    Search GeneIP for patents involving IRF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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