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    Irf1 interferon regulatory factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 16362, updated on 28-Oct-2024

    Summary

    Official Symbol
    Irf1provided by MGI
    Official Full Name
    interferon regulatory factor 1provided by MGI
    Primary source
    MGI:MGI:96590
    See related
    Ensembl:ENSMUSG00000018899 AllianceGenome:MGI:96590
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Irf-1
    Summary
    Enables DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Involved in several processes, including defense response to symbiont; regulation of T cell activation; and regulation of gene expression. Acts upstream of or within CD8-positive, alpha-beta T cell differentiation; positive regulation of interleukin-12 production; and positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Is expressed in several structures, including bone marrow; early conceptus; eye; genitourinary system; and gut. Human ortholog(s) of this gene implicated in asthma; lung cancer (multiple); primary immunodeficiency disease; smallpox; and stomach cancer (multiple). Orthologous to human IRF1 (interferon regulatory factor 1). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in large intestine adult (RPKM 53.2), colon adult (RPKM 41.6) and 20 other tissues See more
    Orthologs
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    Genomic context

    See Irf1 in Genome Data Viewer
    Location:
    11 B1.3; 11 32.0 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (53660841..53669200)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (53770014..53778374)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene interleukin 5 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53568511-53568694 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53576931-53577191 Neighboring gene STARR-positive B cell enhancer ABC_E6982 Neighboring gene STARR-positive B cell enhancer ABC_E10675 Neighboring gene microRNA 7671 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53608789-53608996 Neighboring gene predicted gene 12216 Neighboring gene STARR-seq mESC enhancer starr_29497 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53659189-53659448 Neighboring gene predicted gene, 30785 Neighboring gene solute carrier family 22 (organic cation transporter), member 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (3) 
    • Endonuclease-mediated (6) 
    • Targeted (4)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within CD8-positive, alpha-beta T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in canonical NF-kappaB signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to interferon-beta IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to interferon-beta ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to interleukin-1 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to peptide hormone stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to tumor necrosis factor ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in defense response to virus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in defense response to virus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in immune system process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of T-helper 2 cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of regulatory T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of tyrosine phosphorylation of STAT protein ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of T-helper 1 cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interferon-beta production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of interferon-beta production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of interleukin-12 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of interleukin-12 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of natural killer cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of type I interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of CD8-positive, alpha-beta T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of MyD88-dependent toll-like receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of adaptive immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of innate immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in response to growth hormone ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within toll-like receptor 3 signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in type II interferon-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IC
    Inferred by Curator
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    interferon regulatory factor 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001159393.1NP_001152865.1  interferon regulatory factor 1 isoform b

      See identical proteins and their annotated locations for NP_001152865.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK152193, BY266109
      Consensus CDS
      CCDS48796.1
      UniProtKB/TrEMBL
      Q3U5M1, Q4FK18
      Related
      ENSMUSP00000104550.2, ENSMUST00000108922.9
      Conserved Domains (1) summary
      pfam00605
      Location:7112
      IRF; Interferon regulatory factor transcription factor
    2. NM_001159396.1NP_001152868.1  interferon regulatory factor 1 isoform a

      See identical proteins and their annotated locations for NP_001152868.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' non-coding exon, compared to variant 1, and encodes the longer isoform (a). Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK152005, BE950981, BY328342
      Consensus CDS
      CCDS24686.1
      UniProtKB/Swiss-Prot
      P15314
      UniProtKB/TrEMBL
      Q4FK18, Q5SX13
      Related
      ENSMUSP00000019043.7, ENSMUST00000019043.13
      Conserved Domains (1) summary
      pfam00605
      Location:7112
      IRF; Interferon regulatory factor transcription factor
    3. NM_008390.2NP_032416.1  interferon regulatory factor 1 isoform a

      See identical proteins and their annotated locations for NP_032416.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK152005, BE950981, BY266109
      Consensus CDS
      CCDS24686.1
      UniProtKB/Swiss-Prot
      P15314
      UniProtKB/TrEMBL
      Q4FK18, Q5SX13
      Related
      ENSMUSP00000104548.3, ENSMUST00000108920.10
      Conserved Domains (1) summary
      pfam00605
      Location:7112
      IRF; Interferon regulatory factor transcription factor

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      53660841..53669200
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036156347.1XP_036012240.1  interferon regulatory factor 1 isoform X1